The Genus Corynebacterium in the Genomic Era

This chapter will address the main omics approaches used in studies involving the genus Corynebacterium, Gram-positive microorganisms that can be isolated from many diverse environments. Currently, the genus Corynebacterium has more than 130 highly diversified species, many of which present medical, veterinary and biotechnological importance, such as C. diphtheriae, C. pseudotuberculosis, C. ulcerans and C. glutamicum. Due to the wide application in these fields, several omics methodologies are used to better elucidate the species belonging to this genus, such as genomics, transcriptomics and proteomics. The genomic era has contributed to the development of more advanced and complex approaches that enable the increase of generated data, and consequently the advance on the structural, functional and dynamic knowledge of biological systems

Prediction of new gene products and characterization of hypothetical proteins of Bifidobacterium breve DS15-17 In Silico / Predição de novos produtos gênicos e caracterização de proteínas hipotéticas de Bifidobacterium breve DS15-17 In Silico

The representation of the gene content of an organism is impacted by several factors, ranging from sampling to sequencing and then the genome assembly task. The genome assembly process can generate errors that are related to insufficient coverage in the data set, an inadequate assembly methodology, and finally, errors related to the limitation of the assembly software used. Thus, some genes remain unidentified both in complete and draft genomes, this incomplete gene knowledge impacts on several organisms, mainly of medical and industrial interest, such as Bifidobacterium breve, a Gram-positive bacterium, found in the gastrointestinal microbiota of mammals, including humans, and has beneficial probiotic activities. Therefore, the objective of this work is to identify the new gene products not represented in the genome of Bifidobacterium breve DS15-17 using the raw reads of this organism. The reads were produced from the sequencing with the Illumina MiSeq platform. PAN2HGENE software was used to identify new gene products. After the analysis, 44 new gene products were identified, 26 with described function and 18 hypothetical proteins. The hypothetical proteins identified were analyzed in the ProtoNet and Superfamily databases

Fatores de risco para infecção por pseudomonas aeruginosa em relação à infecções hospitalares / Risk factors for pseudomonas aeruginosa infection in relation to hospital infections

Pseudomonas aeruginosa é uma bactéria gram-negativa, bacilo e aeróbica. Apresenta uma ampla distribuição no ambiente, como solo e água, entretanto consegue colonizar seres humanos, sendo considerado um patógeno oportunista. Mais de 70% das infecções por P. aeruginosa ocorrem com infecções nosocomiais ou associadas à saúde. Assim, o objetivo deste trabalho foi avaliar, com base em resultados de pesquisas científicas, quais são os fatores de risco associados à infecção por P. aeruginosa em relação às infecções hospitalares. Dessa forma, foi realizado um levantamento bibliográfico, entre os anos de 2009 a 2019, nas bases de dados SciELO e PubMed, a partir dos descritores: “Pseudomonas aeruginosa”, “Infecção Hospitalar (Cross Infection)” e “Centros de Saúde (Health Centers)”. Nessa revisão, foi possível identificar uma alta prevalência de aquisição de P. aeruginosa por meio de diversos fatores como: ventilação mecânica, procedimentos invasivos e tratamento inadequado com uso de antibióticos. Conclui-se que os fatores de risco mais prevalentes são, ventilação mecânica, procedimentos invasivos e tratamento inadequado com uso de antibióticos principalmente carbapenem. Além de outros fatores como tempo de internação, condição clínica do paciente, como doenças neurológicas, hematológicas, uso de imunossupressores e colonização prévia do paciente sendo este um fator individual.

Frequência de dengue na Região de Integração de Carajás, Pará, Brasil, entre os anos de 2009 a 2019/ Dengue frequency in the Carajás Integration Region, Pará, Brazil, between the years 2009 and 2019

A região de integração de Carajás é caracterizada pelo intenso fluxo de migração e crescimento acentuado de centros urbanos, com déficit de saneamento básico e infraestrutura. Devido a esses fatores, é considerada região de alto risco para a incidência da dengue. Esta pesquisa objetiva analisar a frequência de casos de dengue, no período de 2009 a 2019, nos municípios da região de integração de Carajás, Pará, Brasil. Para isso, foi feito um estudo epidemiológico acerca dos casos de dengue utilizando os dados do SINAN (Sistema de Informação de Agravos de Notificação). As variáveis consideradas foram os municípios de notificação, sexo, faixa etária e escolaridade. O total de casos de dengue notificados nesse período, na região de Carajás, foi 15.435. A faixa etária com maior número de notificações foi de 20 a 39 anos, as maiores frequências foram nos municípios de Parauapebas e Marabá e o período de maior incidência da doença foi entre os meses de fevereiro e março, época de grande volume de chuva no local. O vasto número de dados ignorados destaca a necessidade de atualização do sistema de informação e preparo dos agentes responsáveis. As características climáticas da região amazônica favorecem o desenvolvimento de arboviroses e a dinâmica entre os fatores ambientais e o vetor indicam o caráter multifatorial da doença

Whole-genome sequence of Corynebacterium pseudotuberculosis 262 biovar equi isolated from cow milk

We report the complete genome sequence of Corynebacterium pseudotuberculosis 262, isolated from a bovine host. C. pseudotuberculosis is an etiological agent of diseases with medical and veterinary relevance. The genome contains 2,325,749 bp, 52.8% G C content, 2,022 coding sequences (CDS), 50 pseudogenes, 48 tRNAs, and 12 rRNAs

Resistome in Lake Bolonha, Brazilian Amazon: Identification of Genes Related to Resistance to Broad-Spectrum Antibiotics

Resistance to antibiotics is one of the most relevant public health concerns in the world. Aquatic environments play an important role because they are reservoirs for antibiotic resistance genes and antibiotic-resistant strains, contributing to the spread of resistance. The present study investigated the resistome in Lake Bolonha (three sampling sites) in the Amazon region using a metagenomics approach and culture-dependent methods. Whole-metagenome-based results showed that the most abundant phyla were Protobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. The composition of the resistome demonstrated that the genes that confer resistance to β-lactams were prevalent at all sampling sites, followed by genes conferring resistance to aminoglycosides and tetracycline. Acquired genes encoding extended-spectrum β-lactamases (e.g., bla CTX-M) and resistance to carbapenems (e.g., bla IMP and bla VIM) were detected through metagenome analysis. Bacteria were isolated from culture medium supplemented with cefotaxime or imipenem, and isolates were identified and analyzed for their antibiotic susceptibility profiles and resistance genes. In total, 98 bacterial isolates belonging to the genera Pseudomonas (37), Acinetobacter (32), Klebsiella (13), Enterobacter (9), Pantoe (3), Stenotrophomonas (3), and Methylobacterium (1) were obtained. Among isolates, the most abundant genes were bla CTX-M (28.3%), bla SHV (22.6%) and bla TEM (18.8%) in isolates from cefotaxime-supplemented medium and bla VIM (28.8%) and bla IMP (22.2%) in isolates recovered from imipenem-supplemented medium. The genes intl1 and intl2 were detected in 19.3% and 7.1% of isolates. Antibiograms showed that 94.9% (from cefotaxime-supplemented medium) and 85.7% (from imipenem-supplemented medium) of the isolates were multidrug resistant. Besides cefotaxime and imipenem, isolates were mostly resistant to aztreonam (91.8%), amoxicillin (98.8%), ampicillin (82.6%), and nalidixic acid (77.5%). Hence, the present study demonstrates that Lake Bolonha is a reservoir of bacteria resistant to antibiotics and resistance genes, some of which are of critical importance to human health

Quadruplex PCR assay for identification of Corynebacterium pseudotuberculosis differentiating biovar Ovis and Equi.

BackgroundCorynebacterium pseudotuberculosis is classified into two biovars, nitrate-negative biovar Ovis which is the etiologic agent of caseous lymphadenitis in small ruminants and nitrate-positive biovar Equi, which causes abscesses and ulcerative lymphangitis in equines. The aim of this study was to develop a quadruplex PCR assay that would allow simultaneous detection and biovar-typing of C. pseudotuberculosis.MethodsIn the present study, genomes of C. pseudotuberculosis strains were used to identify the genes involved in the nitrate reduction pathway to improve a species identification three-primer multiplex PCR assay. The nitrate reductase gene (narG) was included in the PCR assay along with the 16S, rpoB and pld genes to enhance the diagnosis of the multiplex PCR at biovar level.ResultsA novel quadruplex PCR assay for C. pseudotuberculosis species and biovar identification was developed. The results of the quadruplex PCR of 348 strains, 346 previously well-characterized clinical isolates of C. pseudotuberculosis from different hosts (goats, sheep, horse, cattle, buffalo, llamas and humans), the vaccine strain 1002 and the type strain ATCC 19410T, were compared to the results of nitrate reductase identification by biochemical test. The McNemar's Chi-squared test used to compare the two methods used for C. pseudotuberculosis biovar identification showed no significant difference (P = 0.75) [95% CI for odds ratio (0.16-6.14)] between the quadruplex PCR and the nitrate biochemical test. Concordant results were observed for 97.13% (338 / 348) of the tested strains and the kappa value was 0.94 [95% CI (0.90-0.98)].ConclusionsThe ability of the quadruplex assay to discriminate between C. pseudotuberculosis biovar Ovis and Equi strains enhances its usefulness in the clinical microbiology laboratory

Draft genome sequence of Psychrobacter sp. ENNN9_III, a strain isolated from water in a polluted temperate estuarine system (Ria de Aveiro, Portugal)

The genus Psychrobacter includes Gram-negative coccobacilli that are non-pigmented, oxidase-positive, non-motile, psychrophilic or psychrotolerant, and halotolerant. Psychrobacter strain ENNN9_III was isolated from water in a polluted temperate estuarine system, contaminated with hydrocarbons and heavy metals. The genome has a G + C content of 42.7%, 2618 open reading frames (ORFs), three copies of the rRNAs operon, and 29 tRNA genes. Twenty-five sequences related to the degradation of aromatic compounds were predicted, as well as numerous genes related to resistance to metals or metal(loid)s. The genome sequence of Psychrobacter strain ENNN9_III provides the groundwork for further elucidation of the mechanisms of metal resistance and aromatic compounds degradation. Future studies are needed to confirm the usefulness of this strain for bioremediation proposes

CODON-Software to manual curation of prokaryotic genomes.

Genome annotation conceptually consists of inferring and assigning biological information to gene products. Over the years, numerous pipelines and computational tools have been developed aiming to automate this task and assist researchers in gaining knowledge about target genes of study. However, even with these technological advances, manual annotation or manual curation is necessary, where the information attributed to the gene products is verified and enriched. Despite being called the gold standard process for depositing data in a biological database, the task of manual curation requires significant time and effort from researchers who sometimes have to parse through numerous products in various public databases. To assist with this problem, we present CODON, a tool for manual curation of genomic data, capable of performing the prediction and annotation process. This software makes use of a finite state machine in the prediction process and automatically annotates products based on information obtained from the Uniprot database. CODON is equipped with a simple and intuitive graphic interface that assists on manual curation, enabling the user to decide about the analysis based on information as to identity, length of the alignment, and name of the organism in which the product obtained a match. Further, visual analysis of all matches found in the database is possible, impacting significantly in the curation task considering that the user has at his disposal all the information available for a given product. An analysis performed on eleven organisms was used to test the efficiency of this tool by comparing the results of prediction and annotation through CODON to ones from the NCBI and RAST platforms

Complete genome sequence of Corynebacterium pseudotuberculosis strain E19, isolated from a horse in Chile

Corynebacterium pseudotuberculosis is related to several diseases infecting horses and small ruminants, causing economic losses to agribusiness. Here, we present the genome sequence of C. pseudotuberculosis strain E19. The genome includes one circular chromosome 2,367,956 bp (52.1% G+C content), with 2,112 genes predicted, 12 rRNAs, and 48 tRNA