Search

Bifidobacterium breve is among the first microorganisms colonizing the intestinal tract in humans and is a predominant species in the gut microbiota of newborns and children. This bacterium is widely used in the probiotic industry due to its capacity to improve host health. The search for new targets with probiotic properties is an increasing trend with the help of next-generation sequencing as they facilitate the characterization of the bacterial features. B. breve 1101A was isolated from the faeces of healthy children in Brazil and therefore could play a protective role in the gut. To investigate the beneficial properties of this strain, the present study performed a comprehensive characterization of the genetic features involved in the bacterium resistance and adaptation to gastrointestinal conditions, production of nutrients, and immunomodulatory compounds. Furthermore, this study carried out the prediction of genomic elements (plasmids, prophages, CRISPR-Cas systems, insertion sequences, genomic islands, antibiotic resistance genes) to evaluate the safety of B. breve 1101A. A comparative genomics approach using 45 B. breve complete genomes based on pangenome and phylogenomic analysis was also performed to identify specific genes in B. breve 1101A. The prediction of genetic elements, possibly safety-related, did not detect plasmids, but only one incomplete prophage, two non-functional CRISPR systems, and seven genomic islands. Additionally, three antibiotic resistance genes were identified: ileS (resistance to mupirocin), rpoB, and erm(X). In the comparative genomic analysis, the pangenome was revealed to be open, and B. breve 1101A presented 63 unique genes associated with several processes, such as transmembrane transport, membrane components, DNA processes, and carbohydrate metabolism. In conclusion, B. breve 1101A is potentially safe and well-adapted for intestinal disorder therapeutics, although the role of its unique genetic repertoire needs further investigation.

Treponema pallidum subspecies pallidum causes syphilis, a sexually transmitted disease that infects more than 2.1 million pregnant women every year. Due to its maximum death rates and augmented risk of human immunodeficiency virus (HIV) infection, the disease is still a matter of debate in many low- and high-income countries. The infection has three stages that lead to several complications if left untreated and can lead to many tertiary complications in the brain, eyes, ears, heart, and pregnancy. Neurosyphilis is also known as the clinical result of infection of the central nervous system by Treponema pallidum subspecies pallidum. It can evolve at any time and from any stage of syphilis exposure. This review briefly explains the severe and multiple neurosyphilitic complications and recently identified cases related to neurosyphilis. We also explained computational neuroscience, neuroinformatics, and in silico models and techniques based on artificial intelligence and other computational and mathematical methods. These techniques have already been applied to several neurological and psychological brain complications and can be applied to neurosyphilis to better understand the persistence of the disease related to the brain that causes neurosyphilis.

Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015–2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses., Here, the authors present results of the ZiBRA-2 project (https://www.zibra2project.org) which is an arbovirus surveillance project, across the Midwest of Brazil using a mobile genomics laboratory, combined with a genomic surveillance training program that targeted post-graduate students, laboratory technicians, and health practitioners in universities and laboratories.

Lactobacillus delbrueckii subsp. lactis CIDCA is a new potential probiotic strain whose molecular basis attributed to the host’s benefit has been reported. This study investigated the safety aspects of Lactobacillus delbrueckii subsp. lactis CIDCA 133 based on whole-genome sequence and phenotypic analysis to avoid future questions about the harmful effects of this strain consumption. Genomic analysis showed that L. delbrueckii subsp. lactis CIDCA 133 harbors virulence, harmful metabolites, and antimicrobial resistance-associated genes. However, none of these genetic elements is flanked or located within prophage regions and plasmid sequence. At a phenotypic level, it was observed L. delbrueckii subsp. lactis CIDCA 133 antimicrobial resistance to aminoglycosides streptomycin and gentamicin antibiotics, but no hemolytic and mucin degradation activity was exhibited by strain. Furthermore, no adverse effects were observed regarding mice clinical and histopathological analysis after the strain consumption (5 × 107 CFU/mL). Overall, these findings reveal the safety of Lactobacillus delbrueckii subsp. lactis CIDCA 133 for consumption and future probiotic applications.

Within the pathogenic bacterial speciesForty genomes were sampled to represent species, subspecies or biovars ofNineteen genes were detected in the species

The number of draft genomes deposited in Genbank from the National Center for Biotechnology Information (NCBI) is higher than the complete ones. Draft genomes are assemblies that contain fragments of misassembled regions (gaps). Such draft genomes present a hindrance to the complete understanding of the biology and evolution of the organism since they lack genomic information. To overcome this problem, strategies to improve the assembly process are developed continuously. Also, the greatest challenge to the assembly progress is the presence of repetitive DNA regions. This article highlights the use of optical mapping, to detect and correct assembly errors in Corynebacterium pseudotuberculosis. We also demonstrate that choosing a reference genome should be done with caution to avoid assembly errors and loss of genetic information.

The aim of the study was to evaluate the genotypic and phenotypic characteristics of 20 strains of S. Heidelberg (SH) isolated from broilers produced in southern Brazil. The similarity and presence of genetic determinants linked to virulence, antimicrobial resistance, biofilm formation, and in silico-predicted metabolic interactions revealed this serovar as a threat to public health. The presence of the ompC, invA, sodC, avrA, lpfA, and agfA genes was detected in 100% of the strains and the luxS gene in 70% of them. None of the strains carries the blaSHV, mcr-1, qnrA, qnrB, and qnrS genes. All strains showed a multidrug-resistant profile to at least three non-β-lactam drugs, which include colistin, sulfamethoxazole, and tetracycline. Resistance to penicillin, ceftriaxone (90%), meropenem (25%), and cefoxitin (25%) were associated with the presence of blaCTX–M and blaCMY–2 genes. Biofilm formation reached a mature stage at 25 and 37°C, especially with chicken juice (CJ) addition. The sodium hypochlorite 1% was the least efficient in controlling the sessile cells. Genomic analysis of two strains identified more than 100 virulence genes and the presence of resistance to 24 classes of antibiotics correlated to phenotypic tests. Protein-protein interaction (PPI) prediction shows two metabolic pathways correlation with biofilm formation. Virulence, resistance, and biofilm determinants must be constant monitoring in SH, due to the possibility of occurring infections extremely difficult to cure and due risk of the maintenance of the bacterium in production environments.

Lactobacillus delbrueckii subsp. lactis CIDCA 133 (CIDCA 133) has been reported as a potential probiotic strain, presenting immunomodulatory properties. This study investigated the possible genes and molecular mechanism involved with a probiotic profile of CIDCA 133 through a genomic approach associated with in vitro and in vivo analysis. Genomic analysis corroborates the species identification carried out by the classical microbiological method. Phenotypic assays demonstrated that the CIDCA 133 strain could survive acidic, osmotic, and thermic stresses. In addition, this strain shows antibacterial activity against Salmonella Typhimurium and presents immunostimulatory properties capable of upregulating anti-inflammatory cytokines Il10 and Tgfb1 gene expression through inhibition of Nfkb1 gene expression. These reported effects can be associated with secreted, membrane/exposed to the surface and cytoplasmic proteins, and bacteriocins-encoding genes predicted in silico. Furthermore, our results showed the genes and the possible mechanisms used by CIDCA 133 to produce their beneficial host effects and highlight its use as a probiotic microorganism.

The bacterial strain PO100/5 was isolated from a skin abscess of a pig (Sus scrofa domesticus) in the Alentejo region of southern Portugal. It was identified as Corynebacterium pseudotuberculosis using biochemical tests, multiplex PCR and Pulsed Field Gel Electrophoresis. After genome sequencing and rpoB phylogeny, the strain was classified as C. ulcerans. To better understand the taxonomy of this strain and improve identification methods, we compared strain PO100/5 to other publicly available genomes from the C. diphtheriae group. Taxonomic analysis reclassified it and three others strains as belonging to the recently described C. silvaticum, which have been isolated from wild boar and roe deer in Germany and Austria. The results showed that PO100/5 is the first sequenced genome of a C. silvaticum strain from a domestic animal and a different geographical region, is a putative producer of the diphtheriae toxin, and has a unique sequence type. Genomic analysis of PO100/5 showed four prophages and eight conserved genomic islands when compared to C. ulcerans. Pangenome analysis of 38 C. silvaticum and 76 C. ulcerans samples suggest that C. silvaticum is a clonal species, with 73.6% of conserved genes and a pangenome near to being closed (α > 0.952). 172 conserved genes are unique to C. silvaticum when compared to C. ulcerans, with most related to nutrient uptake and metabolism, prophages or immune evasion. These unique genes could be used as genetic markers for species identification. This information can be useful for identification and surveillance of this pathogen, especially in regard to the possibility of zoonotic transmission.

Bacteria of the genusGlutamicibacterare considered ubiquitous because they can be found in soil, water and air. They have already been isolated from different habitats, including different types of soil, clinical samples, cheese and plants. Glutamicibacter creatinolyticus is a Gram-positive bacterium important to various biotechnological processes, however, as a pathogen it is associated to urinary tract infections and bacteremia. Recently,Glutamicibacter creatinolyticusLGCM 259 was isolated from a mare, which displayed several diffuse subcutaneous nodules with heavy vascularization. In this study, sequencing, genomic analysis ofG. creatinolyticusLGCM 259 and comparative analyseswere performedamong 4representatives of different members of genusfromdifferent habitats, available in the NCBI database. The LGCM 259 strain's genome carries important factors of bacterial virulence that are essential in cell viability, virulence, and pathogenicity. Genomic islands were predicted for 4 members of genusGlutamicibacter,showing ahigh number of GEIs,which may reflect a high interspecific diversity and a possible adaptive mechanism responsible for the survival of each species in its specific niche. Furthermore,G. creatinolyticusLGCM 259 sharessyntenicregions, albeit with a considerable loss of genes, in relation to the other species. In addition,G. creatinolyticusLGCM 259 presentsresistancegenes to 6 differentclasses ofantibiotics and heavy metals, such as: copper, arsenic, chromium and cobalt-zinc-cadmium.Comparative genomicsanalysescouldcontribute to the identification of mobile genetic elements particular to the speciesG. creatinolyticuscompared to other members of genus. The presence of specific regions inG. creatinolyticuscould be indicative of their rolesin host adaptation, virulence, and the characterization ofastrain that affects animals.

1. Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. 2. Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil. 3. Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil. 4. Laboratory of Clinical Pathology, Hospital das Clinicas, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. 5. Tiradentes University, Technology and Research Institute, Biomaterials Laboratory, Aracaju, Sergipe, Brazil. 6. Swedish University of Agricultural Sciences, Uppsala, Sweden. 7. Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia, 23284, USA. 8. Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal 721137, India. 9. Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. 10. AQUACEN – National Reference Laboratory of Aquatic Animal Disease, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. 11. Institute of Veterinary Medicine, University of Gottingen, Burckhardtweg 2, Gottingen, Germany. 12. Goncalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia, Brazil.

Klebsiella pneumoniae é uma bactéria Gram-negativa, sem motilidade, em forma de bastonete e encapsulada, que habita vários nichos ecológicos, variando do solo à água. É também um dos patógenos humanos mais importantes, emergindo como agente de graves infecções. Uma análise abrangente do genoma desse microrganismo tem o potencial de fornecer uma melhor compreensão das bases moleculares de sua virulência e patogênese, contribuindo para novas formas de controle da doença. Neste estudo, sequenciamos o genoma de uma linhagem de K. pneumoniae multirresistente, denominada B31, que foi isolada do lavado broncoalveolar de uma paciente admitida em uma unidade de terapia intensiva, no Brasil. As sequências de DNA obtidas da linhagem B31, a partir do sequenciamento Illumina, foram montadas usando uma abordagem ab initio, resultando em um cromossomo de 5,27 Mb. Um multireplicon (IncFIIk / IncFIBk), provavelmente pertencente a um plasmídeo conjugativo, e um replicon IncI1, que pertence a um segundo plasmídeo, foram encontrados usando a ferramenta PlasmidFinder. Comparações genômicas foram conduzidas entre a linhagem B31, outro isolado clínico do Brasil (Kp13), e outros 171 isolados clínicos cujas sequências completas foram recuperadas do banco de dados do NCBI. B31 foi encontrada como sendo pertencente ao Sequence type 15 (ST15), um dos 52 STs encontrados dentre as 173 linhagens analisadas. A busca por genes de resistência revelou que todas as linhagens selecionadas contêm pelo menos um gene codificante de beta-lactamase de espectro estreito (bla). Análises comparativas adicionais foram conduzidas com 44 linhagens representativas de K. pneumoniae, escolhidas com base em resultados filogenômicos e caracterização por MLST. A identificação dos genomas central e acessório foi realizada para caracterizar a conexão entre todas as linhagens analisadas. Este estudo fornece informações genômicas que podem ser úteis para auxiliar na identificação de novas drogas e no desenvolvimento de vacinas contra esse patógeno com implicações na saúde pública. Klebsiella pneumoniae is a Gram-negative, non-motile, rod-shaped, and encapsulated bacterium that dwells in various ecological niches, ranging from soil to water. It is also one of the most important human pathogens, emerging as an agent of severe community infections. A comprehensive analysis of the genome of this microorganism could provide a better understanding of the molecular basis of its virulence and pathogenesis, contributing to new forms of disease control. In this study, we sequenced the genome of a multidrug resistant K. pneumoniae strain, herein named B31, that was isolated from the bronchoalveolar lavage of a patient admitted to an intensive care unit, in Brazil. The DNA sequences obtained from strain B31, with the Illumina sequencing technology, were assembled to form a 5.27-Mb sized genome, using an ab initio approach. A plasmid multireplicon (IncFIIk/ IncFIBk), likely to belong to a conjugative plasmid, and a replicon IncI1, which belongs to a second plasmid, were found using the PlasmidFinder tool. Genomic comparisons were conducted among strain B31, another clinical isolate from Brazil (KP13), and other 171 clinical isolates whose complete genome sequences could be retrieved from the NCBI database. B31 was found to belong to the sequence type 15 (ST15), one out of the 52 sequence types (STs) characterizing the 173 strains analyzed. An in-silico screening of resistance genes revealed that all selected strains harbor at least one narrow-spectrum beta-lactamase (bla) gene. Further comparative analyses were conducted with, 44 representative K. pneumoniae strains, chosen based on phylogenomics and MLST results. The identification of the core and accessory genes was conducted to disclose the connection among all analyzed strains. This study provides genomic information that might be useful to aid in the design of new drugs and vaccines against a pathogen with public health implications.