Intraclonal Genome Stability of the Metallo-beta-lactamase SPM-1-producing Pseudomonas aeruginosa ST277, an Endemic Clone Disseminated in Brazilian Hospitals

Carbapenems represent the mainstay therapy for the treatment of serious P aeruginosa infections. However, the emergence of carbapenem resistance has jeopardized the clinical use of this important class of compounds. The production of SPM-1 metallo-beta-lactamase has been the most common mechanism of carbapenem resistance identified in P. aeruginosa isolated from Brazilian medical centers. Interestingly, a single SPM-1-producing P. aeruginosa clone belonging to the ST277 has been widely spread within the Brazilian territory. In the current study, we performed a next-generation sequencing of six SPM-1-producing P. aeruginosa ST277 isolates. The core genome contains 5899 coding genes relative to the reference strain P. aeruginosa PAO1. A total of 26 genomic islands were detected in these isolates. We identified remarkable elements inside these genomic islands, such as copies of the bla(spM-1) gene conferring resistance to carbapenems and a type I-C CRISPR-Cas system, which is involved in protection of the chromosome against foreign DNA. In addition, we identified single nucleotide polymorphisms causing amino acid changes in antimicrobial resistance and virulence-related genes. Together,these factors could contribute to the marked resistance and persistence of the SPM-1-producing P aeruginosa ST277 clone. A comparison of the SPM-1-producing P. aeruginosa ST277 genomes showed that their core genome has a high level nucleotide similarity and synteny conservation. The variability observed was mainly due to acquisition of genomic islands carrying several antibiotic resistance genes.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Lab Nacl Comp Cient, Lab Bioinformat, Petropolis, BrazilUniv Fed Sao Paulo, Escola Paulista Med, Dept Internal Med, Lab Alerta,Div Infect Dis, Sao Paulo, BrazilLaboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, BrazilCNPq: 305535/2014-5CNPq: 302768/2011-4CNPq: 312864/2015-9FAPERJ: E-26/202.903/2016Web of Scienc

Complete genome sequence of Burkholderia phenoliruptrix BR3459a (CLA1), a heat-tolerant, nitrogen-fixing symbiont of mimosa flocculosa.

The genus Burkholderia represents a challenge to the fields of taxonomy and phylogeny and, especially, to the understanding of the contrasting roles as either opportunistic pathogens or bacteria with biotechnological potential. Few genomes of nonpathogenic strains, especially of diazotrophic symbiotic bacteria, have been sequenced to improve understanding of the genus. Here, we contribute with the complete genome sequence of Burkholderia phenoliruptrix strain BR3459a (CLA1), an effective diazotrophic symbiont of the leguminous tree Mimosa flocculosa Burkart, which is endemic to South America

The complete genome of Burkholderia phenoliruptrix strain BR3459a, a symbiont of Mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes.

Burkholderia species play an important ecological role related to xenobiosis, the promotion of plant growth, the biocontrol of agricultural diseases, and symbiotic and non-symbiotic biological nitrogen fixation. Here, we highlight our study as providing the first complete genome of a symbiotic strain of B. phenoliruptrix, BR3459a (=CLA1), which was originally isolated in Brazil from nodules of Mimosa flocculosa and is effective in fixing nitrogen in association with this leguminous species. Genomic comparisons with other pathogenic and non-pathogenic Burkholderia strains grouped B. phenoliruptrix BR3459a with plant-associated beneficial and environmental species, although it shares a high percentage of its gene repertoire with species of the B. cepacia complex (Bcc) and "pseudomallei" group. The genomic analyses showed that the bce genes involved in exopolysaccharide production are clustered together in the same genomic region, constituting part of the Group III cluster of non-pathogenic bacteria. Regarding environmental stresses, we highlight genes that might be relevant in responses to osmotic, heat, cold and general stresses. Furthermore, a number of particularly interesting genes involved in the machinery of the T1SS, T2SS, T3SS, T4ASS and T6SS secretion systems were identified. The xenobiotic properties of strain BR3459a were also investigated, and some enzymes involved in the degradation of styrene, nitrotoluene, dioxin, chlorocyclohexane, chlorobenzene and caprolactam were identified. The genomic analyses also revealed a large number of antibiotic-related genes, the most important of which were correlated with streptomycin and novobiocin. The symbiotic plasmid showed high sequence identity with the symbiotic plasmid of B. phymatum. Additionally, comparative analysis of 545 housekeeping genes among pathogenic and non-pathogenic Burkholderia species strongly supports the definition of a new genus for the second branch, which would include BR3459a. The analyses of B. phenoliruptrix BR3459a showed key property of fixing nitrogen that together with genes for high tolerance to environmental stresses might explain a successful strategy of symbiosis in the tropics. The strain also harbours interesting sets of genes with biotechnological potential. However, the resemblance of certain genes to those of pathogenic Burkholderia raise concerns about large-scale applications in agriculture or for bioremediation

A nested-PCR assay for detection of Xylella fastidiosa in citrus plants and sharpshooter leafhoppers

Aims: Detection of Xylella fastidiosa in citrus plants and insect vectors.Methods and Results: Chelex 100 resin matrix was successfully standardized allowing a fast DNA extraction of X. fastidiosa. An amplicon of 500 bp was observed in samples of citrus leaf and citrus xylem extract, with and without symptoms of citrus variegated chlorosis, using PCR with a specific primer set indicating the presence of X. fastidiosa. The addition of insoluble acid-washed polyvinylpyrrolidone (PVPP) prior to DNA extraction of insect samples using Chelex 100 resin together with nested-PCR permitted the detection of X. fastidiosa within sharpshooter heads with great sensitivity. It was possible to detect up to two bacteria per reaction. From 250 sharpshooter samples comprising four species (Dilobopterus costalimai, Oncometopia facialis, Bucephalogonia xanthopis and Acrogonia sp.), 87 individuals showed positive results for X. fastidiosa in a nested-PCR assay.Conclusions: the use of Chelex 100 resin allowed a fast and efficient DNA extraction to be used in the detection of X. fastidiosa in citrus plants and insect vectors by PCR and nested-PCR assays, respectively.Significance and Impact of the study: the employment of efficient and sensitive methods to detect X. fastidiosa in citrus plants and insect vectors will greatly assist epidemiological studies

Spectrophotometric determination of diclofenac in pharmaceutical preparations assisted by microwave oven

Neste trabalho é proposto um método eficaz e de baixo custo para a determinação de diclofenaco de sódio (ou potássio) na forma pura e em preparações farmacêuticas. O método é baseado na reação de diclofenaco com tetracloro-p-benzoquinona (p-cloranil) em meio de metanol. Esta reação foi acelerada pela irradiação da mistura reagente com energia microondas (1100W) por 27 segundos, produzindo um complexo de transferência de carga com um máximo de absorção em 535 nm. As condições ótimas da reação, tais como: concentração de reagentes, tempo de aquecimento e a estabilidade do produto da reação foram determinadas. A lei de Beer é obedecida num intervalo de concentração de 1,25x10-4 a 2,00x10-3 mol l-1 com um coeficiente de correlação de 0,9993 e absortividade molar de 0,49x10³ l mol-1 cm-1. O limite de detecção (LOD) do método foi de 1,35x10-5 mol l-1 e o limite de quantificação (LOQ) foi 4,49x10-5 mol l-1. Não foram observadas interferências de substâncias comumente encontradas junto com diclofenaco em preparações farmacêuticas, tais como: glicose, lactose, talco, amido, estearato de magnésio, sulfito de sódio, dióxido de titânio, polietilenoglicol, polivinilpirrolidona, manitol e álcool benzílico. Os resultados analíticos obtidos a partir da aplicação do método proposto estão em muito boa concordância com aqueles obtidos pelo método padrão da Farmacopéia Americana. As recuperações obtidas para o diclofenaco a partir de um estudo com várias preparações farmacêuticas estiveram dentro de 95,9% a 103,3%, com desvio padrão variando de 0,2% a 1,8%.In this work, an effective and low-cost method for the determination of sodium or potassium diclofenac is proposed in its pure form and in their pharmaceutical preparations. The method is based on the reaction between diclofenac and tetrachloro-p-benzoquinone (p-chloranil), in methanol medium. This reaction was accelerated by irradiating of reactional mixture with microwave energy (1100 W) during 27 seconds, producing a charge transfer complex with a maximum absorption at 535 nm. The optimal reaction conditions values such as reagent concentration, heating time and stability of the reaction product were determined. Beer's law is obeyed in a concentration range from of 1.25x10-4 to 2.00x10-3 mol l-1 with a correlation coefficient of 0.9993 and molar absorptivity of 0.49 x10³ l mol-1 cm-1. The limit of detection (LOD) was 1.35x10-5 mol l-1 and the limit of quantification (LOQ) was 4.49x10-5 mol l-1. In the presence of the common excipients, such as glucose, lactose, talc, starch, magnesium stearate, sodium sulphite, titanium dioxide, polyethyleneglycol, polyvinylpirrolidone, mannitol and benzilic alcohol no interferences were observed. The analytical results obtained by applying the proposed method compare very favorably with those given by the United States Pharmacopeia standard procedure. Recoveries of diclofenac from various pharmaceutical preparations were within 95.9% to 103.3%, with standard deviations ranging from 0.2% to 1.8%.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Whole-genome expression profiling of Xylella fastidiosa in response to growth on glucose

Xylella fastidiosa is the etiologic agent of diseases in a wide range of economically important crops including citrus variegated chlorosis, a major threat to the Brazilian citrus industry. The genomes of several strains of this phytopathogen have been completely sequenced enabling large-scale functional studies. In this work we used whole-genome DNA microarrays to investigate the transcription profile of X. fastidiosa grown in defined media with different glucose concentrations. Our analysis revealed that while transcripts related to fastidian gum production were unaffected, colicin-V-like and fimbria precursors were induced in high glucose medium. Based on these results, we suggest a model for colicin-defense mechanism in X. fastidiosa

Complete genome sequence of Burkholderia phenoliruptrix BR3459a (CLA1), a heat-tolerant, nitrogen-fixing symbiont of mimosa flocculosa.

The genus Burkholderia represents a challenge to the fields of taxonomy and phylogeny and, especially, to the understanding of the contrasting roles as either opportunistic pathogens or bacteria with biotechnological potential. Few genomes of nonpathogenic strains, especially of diazotrophic symbiotic bacteria, have been sequenced to improve understanding of the genus. Here, we contribute with the complete genome sequence of Burkholderia phenoliruptrix strain BR3459a (CLA1), an effective diazotrophic symbiont of the leguminous tree Mimosa flocculosa Burkart, which is endemic to South America.201