A real-time quantitative PCR based on molecular beacon for detecting Brucella infection / PCR quantitativo em tempo real, baseado em guia molecular para detecção de infeção por Brucella

O objetivo deste comunicado é desenvolver um método quantitativo PCR em tempo real, baseado em guia molecular (MB) (MB-qPCR) para detecção de infecção por espécies de Brucella, e avaliar seu potencial de utilização clínica. Os primers e as sondas MB foram desenhados para amplificação específica e determinação de sequência conservada do código do gene para os primeiros 58-aa da proteína de membrana externa OMP-2a, que é compartilhada em cinco espécies de Brucella epidêmicas. A avaliação metodológica foi realizada por análise de sensibilidade, especificidade, coeficiente de variação intra e inter, e a linearidade do qPCR. O potencial diagnóstico foi avaliado comparando-se o método qPCR desenvolvido com ensaios de exames bacteriológicos convencionais, incluindo os testes de soroaglutinação convencionais (SATs) e os testes do Rosa Bengala (RBPTs). O método exibiu alta sensibilidade (tão baixo quanto 50 cópias) e grande faixa de linearidade (102-108 cópias). Nenhuma reação cruzada foi encontrada com bactéria clínica comum. A sensibilidade diagnóstica foi superior ao exame bacteriológico, e a especificidade diagnóstica foi superior ao SAT ou ao RBPT. Um método MB-qPCR altamente sensível e específico para DNA de Brucella foi estabelecido com sucesso, provando ser uma ferramenta útil no diagnóstico molecular de brucelose.(AU)

A real-time quantitative PCR based on molecular beacon for detecting Brucella infection / PCR quantitativo em tempo real, baseado em guia molecular para detecção de infeção por Brucella

O objetivo deste comunicado é desenvolver um método quantitativo PCR em tempo real, baseado em guia molecular (MB) (MB-qPCR) para detecção de infecção por espécies de Brucella, e avaliar seu potencial de utilização clínica. Os primers e as sondas MB foram desenhados para amplificação específica e determinação de sequência conservada do código do gene para os primeiros 58-aa da proteína de membrana externa OMP-2a, que é compartilhada em cinco espécies de Brucella epidêmicas. A avaliação metodológica foi realizada por análise de sensibilidade, especificidade, coeficiente de variação intra e inter, e a linearidade do qPCR. O potencial diagnóstico foi avaliado comparando-se o método qPCR desenvolvido com ensaios de exames bacteriológicos convencionais, incluindo os testes de soroaglutinação convencionais (SATs) e os testes do Rosa Bengala (RBPTs). O método exibiu alta sensibilidade (tão baixo quanto 50 cópias) e grande faixa de linearidade (102-108 cópias). Nenhuma reação cruzada foi encontrada com bactéria clínica comum. A sensibilidade diagnóstica foi superior ao exame bacteriológico, e a especificidade diagnóstica foi superior ao SAT ou ao RBPT. Um método MB-qPCR altamente sensível e específico para DNA de Brucella foi estabelecido com sucesso, provando ser uma ferramenta útil no diagnóstico molecular de brucelose.(AU)

Enumeration, antimicrobial resistance and typing of Salmonella enterica: profile of strains carried in the intestinal contents of pigs at slaughter in Southern Brazil

Background: Despite a strong association between Salmonella isolation and slaughter hygiene, as measured by the Enterobacteriaceae levels on pre-chill carcass surfaces, a high variation in this association was observed between sampling dayswithin the same slaughterhouse. It was hypothesised that in a scenario of high exposure on the farm, batches with a highprevalence of carrier pigs shedding a high number of Salmonella may enhance the risk of contamination on some slaughterdays. Thus, the aim of this study was to assess the profile of Salmonella carried in the intestinal contents of slaughter pigs.Materials, Methods & Results: Ten pig batches slaughtered in a slaughterhouse were investigated for the presence ofSalmonella. From each pig, the following samples were taken: i. blood collected at bleeding; ii. sponges rubbed on thecarcass surface after bleeding and before chilling; iii. fragment of the ileocecal region of the intestine. Serum sampleswere subjected to a ELISA-Typhimurium test. Sponges were investigated for the presence of Salmonella and total aerobicmesophilic (TAM) and Enterobacteriaceae (EC) bacterial counts. Salmonella was enumerated in the intestinal contents.Selected Salmonella strains were subjected to an antimicrobial resistance disk diffusion test, macro-restriction with Xba-I(PFGE) and whole genome sequencing (WGS). From the 50 sampled pigs, 96% were positive in the ELISA-Typhimuriumtest and 64% were Salmonella-positive in the intestinal contents. The amount of Salmonella in the intestinal content sampleswas highly variable, and the mean log of fitted distributions of Salmonella in the batch ranged from -2.97 to 2.25 cfu.g-1.The slaughter process achieved a logarithmic reduction, ranging from 0.64 to 2.35 log cfu.cm-2 for TAM and from 0.55 to2.57 log cfu.cm-2 for EC. Salmonella was isolated from 16% of the carcasses after bleeding; this frequency decreased to8% at the pre-chill...

Enumeration, antimicrobial resistance and typing of Salmonella enterica: profile of strains carried in the intestinal contents of pigs at slaughter in Southern Brazil

Background: Despite a strong association between Salmonella isolation and slaughter hygiene, as measured by the Enterobacteriaceae levels on pre-chill carcass surfaces, a high variation in this association was observed between sampling dayswithin the same slaughterhouse. It was hypothesised that in a scenario of high exposure on the farm, batches with a highprevalence of carrier pigs shedding a high number of Salmonella may enhance the risk of contamination on some slaughterdays. Thus, the aim of this study was to assess the profile of Salmonella carried in the intestinal contents of slaughter pigs.Materials, Methods & Results: Ten pig batches slaughtered in a slaughterhouse were investigated for the presence ofSalmonella. From each pig, the following samples were taken: i. blood collected at bleeding; ii. sponges rubbed on thecarcass surface after bleeding and before chilling; iii. fragment of the ileocecal region of the intestine. Serum sampleswere subjected to a ELISA-Typhimurium test. Sponges were investigated for the presence of Salmonella and total aerobicmesophilic (TAM) and Enterobacteriaceae (EC) bacterial counts. Salmonella was enumerated in the intestinal contents.Selected Salmonella strains were subjected to an antimicrobial resistance disk diffusion test, macro-restriction with Xba-I(PFGE) and whole genome sequencing (WGS). From the 50 sampled pigs, 96% were positive in the ELISA-Typhimuriumtest and 64% were Salmonella-positive in the intestinal contents. The amount of Salmonella in the intestinal content sampleswas highly variable, and the mean log of fitted distributions of Salmonella in the batch ranged from -2.97 to 2.25 cfu.g-1.The slaughter process achieved a logarithmic reduction, ranging from 0.64 to 2.35 log cfu.cm-2 for TAM and from 0.55 to2.57 log cfu.cm-2 for EC. Salmonella was isolated from 16% of the carcasses after bleeding; this frequency decreased to8% at the pre-chill...(AU)

Draft genome sequence of Exiguobacterium aurantiacum strain PN47 isolate from saline ponds, known as Salar del Huasco, located in the Altiplano in the North of Chile

In this report, we present a draft genome of 2,886,173 bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named “Salar del Huasco” in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.(AU)

Draft genome sequence of Vitellibacter aquimaris D-24T isolated from seawater

Vitellibacter aquimaris D-24T (=KCTC 42708T = DSM 101732T), a halophilic marine bacterium, was isolated from seawater collected from Desaru beach, Malaysia. Here, we present the draft genome sequence of D-24T with a genome size of approximately 3.1 Mbp and G + C content of 39.93%. The genome of D-24T contains genes involved in reducing a potent greenhouse gas (N2O) in the environment and the degradation of proteinaceous compounds. Genome availability will provide insights into potential biotechnological and environmental applications of this bacterium.(AU)

Complete genome sequence of human pathogen Kosakonia cowanii type strain 888-76T

Kosakonia cowanii type strain 888-76T is a human pathogen which was originally isolated from blood as NIH group 42. In this study, we report the complete genome sequence of K. cowanii 888-76T. 888-76T has 1 chromosome and 2 plasmids with a total genome size of 4,857,567 bp and C+G 56.15%. This genome sequence will not only help us to understand the virulence features of K. cowanii 888-76T but also provide us the useful information for the study of evolution of Kosakonia genus.(AU)

Genome sequence of Streptomyces mangrovisoli MUSC 149T isolated from intertidal sediments

As the largest genus in Actinobacteria family, Streptomyces species have the ability to synthesize numerous compounds of diverse structures with bioactivities. Streptomyces mangrovisoli MUSC 149T was previously isolated as a novel streptomycete from mangrove forest in east coast of Peninsular Malaysia. The high quality draft genome of MUSC 149T comprises 9,165,825 bp with G + C content of 72.5%. Through bioinformatics analysis, 21 gene clusters identified in the genome were associated with the production of bioactive secondary metabolites. The presence of these biosynthetic gene clusters in MUSC 149T suggests the potential exploitation of the strain for production of medically important compounds.(AU)

Draft genome sequence of Chryseobacterium limigenitum SUR2T (LMG 28734T) isolated from dehydrated sludge

The type strain SUR2 of the novel species Chryseobacterium limigenitum was isolated from a dehydrated sludge of the municipal sewage treatment plant in Dogoše near Maribor in Slovenia. The draft genome, with 60 contigs, 4,697,725 bp, 34.4% of G+C content, was obtained using the Illumina HiSeq 2500-1 platform. Joint Genome Institute Microbial Genome Annotation Pipeline (MGAP v.4) has identified 4322 protein-coding sequences including resistance genes against arsenic and other heavy metals. In addition, a subclass B3 metallo-β-lactamase, which confers resistance to penicillins, cephalosporins and carbapenems, was also present in the genome. The genome sequence provides important information regarding bioremediation potential and pathogenic properties of this newly identified species.(AU)

Genome sequencing of two Bacillus anthracis strains: a virulent strain and a vaccinal strain

Bacillus anthracis strain SPV842_15 was isolated from bovine fetus, while B. anthracis strain Brazilian vaccinal was recovered from a commercial vaccine. We report here the genome sequences of both strains. The SPV842_15 genome is composed of a single circular chromosome with a length of 5,228,664 base pairs, and comprises 5911 coding sequences. In turn, the Brazilian vaccinal genome remains in 201 contigs with 5733 coding sequences. Both genomes have an overall C + G content of 35.4%, and 11 genes encoding the ribosomal RNAs (rRNAs) 5S, 16S and 23S. Only the plasmid pX01 sequence, which carries genes for toxins synthesis, was detected and completely assembled for both strains. These plasmids have a length of 181,684 base pairs and a C + G content of 32.5%. These genomic data generate insights about vaccinal B. anthracis virulence.(AU)

Whole genome sequence of lactic acid bacterium Pediococcus acidilactici strain S1

Pediococcus acidilactici strain S1, a lactic acid-fermenting bacterium, was isolated from makgeolli-a Korean traditional fermented alcoholic beverage. Here we report the 1,980,172 bp (G + C content, 42%) genome sequence of Pediococcus acidilactici strain S1 with 1,525 protein-coding sequences (CDS), of which 47% could be assigned to recognized functional genes. The genome sequence of the strain S1 might provide insights into the genetic basis of the lactic acid bacterium with alcohol-tolerant.(AU)

Genome sequencing of four strains of Phylotype I, II and IV of Ralstonia solanacearum that cause potato bacterial wilt in India

Ralstonia solanacearum is a heterogeneous species complex causing bacterial wilts in more than 450 plant species distributed in 54 families. The complexity of the genome and the wide diversity existing within the species has led to the concept of R. solanacearum species complex (RsSC). Here we report the genome sequence of the four strains (RS2, RS25, RS48 and RS75) belonging to three of the four phylotypes of R. solanacearum that cause potato bacterial wilt in India. The genome sequence data would be a valuable resource for the evolutionary, epidemiological studies and quarantine of this phytopathogen.(AU)

Draft genome sequence of a multidrug-resistant beta-lactamase OXA-357-producing Acinetobacter pittii ST865 clinical isolate from China

Worldwide increasing emergence of carbapenem-resistant Acinetobacter spp. has rendered the limited availability of effective antimicrobial agents and has become a major public health concern. In this study, we report the draft genome sequence of A. pittii TCM156, a multidrug-resistant isolate that harbored the blaOXA-357 gene. The genome sequence was further analyzed by various bioinformatics methods. The genome size was estimated to be 3,807,313 bp with 3508 predicted coding regions and G + C content is 38.7%. These findings have raised awareness of the possible emergence of OXA-type enzyme-producing A. pittii isolate in China.(AU)

Draft genome analysis of Dietzia sp. 111N12-1, isolated from the South China Sea with bioremediation activity

Dietzia sp. 111N12-1, isolated from the seawater of South China Sea, shows strong petroleum hydrocarbons degradation activity. Here, we report the draft sequence of approximately 3.7-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Dietzia strain isolated from the sea. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of hydrocarbons degradation in this strain.(AU)

Draft genome of Nocardia farcinica TRH1, a linear and polycyclic aromatic hydrocarbon-degrading bacterium isolated from the coast of Trindade Island, Brazil

Here, we report the draft genome sequence and annotation of Nocardia farcinica TRH1, a petroleum hydrocarbons degrading Actinobacteria isolated from the coastal water of Trindade Island, Brazil.(AU)

Complete genome sequence of the aerobically denitrifying thermophilic bacterium Chelatococcus daeguensis TAD1

ABSTRACT Chelatococcus daeguensis TAD1 is a themophilic bacterium isolated from a biotrickling filter used to treat NOx in Ruiming Power Plant, located in Guangzhou, China, which shows an excellent aerobic denitrification activity at high temperature. The complete genome sequence of this strain was reported in the present study. Genes related to the aerobic denitrification were identified through whole genome analysis. This work will facilitate the mechanism of aerobic denitrification and provide evidence for its potential application in the nitrogen removal.(AU)