Ecosocioeconomics applied to urban freight by bicycle and motorcycle in the city of Curitiba, Brazil

The aim of this work is to compare the logistics of urban light weight delivery by motorcycle and bicycle. To this purpose, a case study in the city of Curitiba, Brazil, was chosen. City planning demands alternative solutions to everyday problems, among which use of urban space and mobility are relevant due to fast and rather chaotic growing. Urban mobility −a complex network comprising a variety of actors and areas; has social, economic and environmental impacts that might be underestimated in planning and implementation of actions. So far, and for the case studied here, urban planning for light weight delivery has not included externalities, but rather focused on technical issues on logistics and urban traffic. For instance, the rates of dead and disability from accidents on this mobility are currently very high. In the present research, two light weight deliveries actually used in Curitiba were compared: motorbikes and bicycles. The analysis is based on the methodology of the eco-socio-economy of organizations. This approach considers the complexity of subsystems linked, and the effectiveness beyond the organization but on the social demands in the urban territory. The use of bicycles was studied using data from EcoBike, analyzed here and compared to the generic case of deliveries by motorbikes. Indicators for accidents (with and without death), fossil energy used, CO2 emissions, and operative costs were obtained and compared. The indicators assessed favour the use of bicycles over motorbikes.Fil: García, M.. Pontifícia Universidade Católica do Paraná; BrasilFil: Sampaio, C. A. C.. Pontifícia Universidade Católica do Paraná; BrasilFil: Gonzalez, Alejandro Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; Argentina. Universidad Nacional del Comahue; Argentin

Draft Genome Sequence of a Pathogenic O86:H25 Sequence Type 57 Escherichia coli Strain Isolated from Poultry and Carrying 12 Acquired Antibiotic Resistance Genes

Free PMC Article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582591/Escherichia coli is a commensal bacterium that is frequently associated with multidrug-resistant zoonotic and foodborne infections. Here, we report the 5.6-Mbp draft genome sequence of an E. coli recovered from poultry, which encodes multiple acquired antibiotic resistance determinants, virulence factors, pathogenicity determinants, and mobile genetic elements.Daniela Jones-Dias and Vera Manageiro have received research funding from Fundação para Ciência e Tecnologia (grant numbers SFRH/BD/ 80001/2011 and SFRH/BPD/77486/2011, respectively). This work was supported by Fundação para a Ciência e a Tecnologia (grant number PEst-OE/AGR/UI0211/2011-2014)

Draft Genome Sequence of the First NDM-1-ProducingProvidencia stuartiiStrain Isolated in Portugal

We report here the draft genome sequence of the first NDM-1-producing Providencia stuartii strain isolated in Portugal. Sequence analyses revealed the presence of an incompatibility group A/C2 (IncA/C2) plasmid and of diverse acquired genes conferring resistance to β-lactams, aminoglycosides, tetracycline, macrolides, chloramphenicol, and sulfonamides. This sequence contributes to the evaluation of the spread of NDM-1 producers.V. Manageiro was supported by grant SFRH/BPD/77486/2011 from the Fundação para a Ciência e a Tecnologia (FCT), Lisbon, Portugal

NDM-1-producing Providencia stuartii isolates in a Portuguese Hospital

Objective: Providencia stuartii is an opportunistic pathogen typically associated with urinary infections, and is intrinsically resistance to a wide range of antibiotics. The main aim of this study was to characterize five carbapenemase (CA) NDM-1-producing P. stuartii isolates obtained during an outbreak detected in a Hospital. Methods: MICs were obtained by the reference microdilution broth method, according to EUCAST guidelines. PCR amplification and DNA sequencing were applied to identify the presence of CA genes from class A, B and D. Direct transfer of the CA resistance phenotype was attempted by mating-out assays. Genetic relatedness was examined by PFGE. One isolate, INSRA21868, recovered from the urine of an 88-year-old male patient admitted to the intensive care unit, was selected for genetic characterization using whole-genome sequencing (WGS), performed using 150 bp paired-end reads on a MiSeq (Illumina). A set of bioinformatic web tools were used to estimate the presence of pathogenicity determinants, antibiotic resistance (AR) genes, and clinically relevant mobile genetic elements. Results: All isolates, genetically indistinguishable by PFGE, presented multidrug-resistance with non-susceptibility to all carbapenems tested. Transconjugants had AR profiles similar to those of their parental clinical isolates. All NDM-1 determinants tested were found to be carried on conjugative plasmids. In silico AR analyses using ResFinder-v2.1 revealed genes conferring resistance to β-lactams [blaNDM-1, blaCMY-4 and ΔblaDHA-1), aminoglycosides (aac(2’)-Ia, armA), tetracycline (tetB), macrolides (mphE and msrE), chloramphenicol (catB3), and sulfonamides (sul1). PlasmidFinder-v1.2 analyses revealed the presence of an IncA/C2, which has been associated with wide dissemination of blaNDM-1. In the 3’ region, the blaNDM-1 gene was adjacent to a bleomycin resistance-encoding gene (bleMBL), followed by a trpF and part of the blaDHA-1-ampR region. The ISAba125 element upstream of blaNDM-1 was interrupted by an IS26 element. Conclusion: This study emphasizes the elements involved in dissemination of nosocomial infections and the potential of WGS in epidemiological investigations in the prevention of CA dissemination among hospitals as well as to other bacterial genera.info:eu-repo/semantics/acceptedVersio

Isolamento de Helicobacter pullorum de carne de frango: características de um patogénio emergente de origem alimentar

Objetivo: Este estudo apresenta a primeira descrição do isolamento de H. pullorum em amostras de carne de frango crua, revelando o importante papel da metodologia de Sequenciação Total do Genoma para a correta identificação e caracterização das estirpes isolada

Legionella pneumophila strain associated with the first evidence of person-to-person transmission of Legionnaires’ disease: a unique mosaic genetic backbone

A first strong evidence of person-to-person transmission of Legionnaires' Disease (LD) was recently reported. Here, we characterize the genetic backbone of this case-related Legionella pneumophila strain ("PtVFX/2014"), which also caused a large outbreak of LD. PtVFX/2014 is phylogenetically divergent from the most worldwide studied outbreak-associated L. pneumophila subspecies pneumophila serogroup 1 strains. In fact, this strain is also from serogroup 1, but belongs to the L. pneumophila subspecies fraseri. Its genomic mosaic backbone reveals eight horizontally transferred regions encompassing genes, for instance, involved in lipopolysaccharide biosynthesis or encoding virulence-associated Dot/Icm type IVB secretion system (T4BSS) substrates. PtVFX/2014 also inherited a rare ~65 kb pathogenicity island carrying virulence factors and detoxifying enzymes believed to contribute to the emergence of best-fitted strains in water reservoirs and in human macrophages, as well as a inter-species transferred (from L. oakridgensis) ~37.5 kb genomic island (harboring a lvh/lvr T4ASS cluster) that had never been found intact within L. pneumophila species. PtVFX/2014 encodes another lvh/lvr cluster near to CRISPR-associated genes, which may boost L. pneumophila transition from an environmental bacterium to a human pathogen. Overall, this unique genomic make-up may impact PtVFX/2014 ability to adapt to diverse environments, and, ultimately, to be transmitted and cause human disease.info:eu-repo/semantics/publishedVersio

Genome Sequencing of 10 Helicobacter pylori Pediatric Strains from Patients with Nonulcer Dyspepsia and Peptic Ulcer Disease

We present draft genome sequences of 10 Helicobacter pylori clinical strains isolated from children. This will be important for future studies of comparative genomics in order to better understand the virulence determinants underlying peptic ulcer disease.This work was supported by the FCT-PTDC/BIM-MEC/1051/2012 grant from the Fundação para a Ciência e a Tecnologia (FCT) (to M.O.). A.N. and F.F.V. are recipients of postdoctoral fellowships (SFRH/BPD/75295/2010 and SFRH/BPD/95125/2013, respectively) from FCT, and R.R. is a recipient of a fellowship (BRJ-DDI/2012) from the National Institute of Health

Vigilância da Gripe em Portugal no inverno 2013/2014

Introdução: O Programa Nacional de Vigilância da Gripe tem como objetivos: recolha, análise e divulgação da informação sobre a atividade gripal em Portugal. A vigilância clínica e laboratorial possibilita a determinação semanal das taxas de incidência de síndroma gripal (SG), identificação/ caracterização do vírus influenza, deteção de surtos, vírus emergentes com potencial pandémico e risco para a saúde pública. Foi analisada e descrita a atividade gripal em Portugal, na época de 2013/2014. Materiais e Métodos: Em 2013/2014, colaboraram: a Rede de Médicos-Sentinela (Rede MS), possibilitando o cálculo da taxa de incidência da síndroma gripal. Na componente laboratorial, colaboram Rede MS, Rede de Serviços-Urgência, médicos projeto-EuroEVA e Rede Portuguesa Laboratórios Diagnóstico Gripe com envio de amostras respiratórias para pesquisa/caraterização do vírus influenza. Resultados: Em 2013/2014, a atividade gripal foi moderada. O período epidémico ocorreu entre as semanas 1/2014 e 8/2014, valor máximo 80,7 casos SG / 100000 habitantes na semana 4/2014. A análise laboratorial a 869 exsudados-nasofaringe permitiu a identificação do vírus influenza em 467 (54%) casos de SG. Destes, 460 (98,5%) do tipo A: 279 (32%) do subtipo A(H1)pdm09 e 181 (21%) do subtipo AH3. Foram detetados 7 vírus influenza do tipo B. Discussão e Conclusão: Na época 2013/2014, a atividade gripal foi moderada com taxas de incidência semelhantes às 2012/2013. O período epidémico ocorreu mais cedo em relação a 2012/2013 e foi de menor duração. O vírus influenza do tipo A foi predominante com co-circulação dos dois subtipos: A(H1)pdm09 e A(H3). Os vírus detetados são genética e antigenicamente semelhantes às estirpes vacinais e sensíveis ao oseltamivir e zanamivir

Probable Person-to-Person Transmission of Legionnaires’ Disease

Correspondence to the Editor.Legionnaires’ disease is an often severe form of pneumonia that is typically acquired by susceptible persons (e.g., elderly persons and smokers) through inhalation of aerosols that contain legionella species.1-4 A cluster of cases of this disease occurred in Vila Franca de Xira, Portugal, in 2014

Accreditation under the International Standard ISO 15189: Experience of a Genetics Laboratory in DNA Sequencing

Introduction: Health care is to some extent influenced by the results of laboratory tests. In order to provide the best care for the patient, laboratories must seek to achieve high levels of quality and competence. International Standard ISO 15189 specifies these requirements and may be used by laboratories to perform accredited genetic tests of materials derived from the human body. Here we describe the procedures to establish Accreditation of DNA sequencing in our laboratory and the first Accreditation of its kind in Portugal. Methods: Our laboratory started to prepare to comply with ISO 15189 Accreditation requirements for DNA sequencing in 2010. Documents describing administrative and technical procedures of the sequencing workflow including sample registries, laboratory protocols, operation and maintenance of equipments, as well as preparation and use of reagents were produced. Regular examination of laboratory equipments by an external entity was implemented to confirm compliance with working requirements. Requisites for personnel training and demonstration of competence were also implemented. The laboratory participated regularly in the DNA sequencing scheme organized by the European Molecular Genetics Quality Network (EMQN). Results: The laboratory obtained formal recognition by Instituto Português de Acreditação (IPAC) in May 2014. A maximum genotyping score for DNA sequencing has been obtained in the external quality assessment scheme since 2010. Sequencing quality measured in terms of the quality read overlap metrics is currently of approximately 96% according to the EMQN scheme. The laboratory processes and analyzes an average of 28.750 samples per year. Discussion: Accreditation of a genetic test under ISO 15189 is a highly demanding and laborious task for a genetic laboratory. However, it is an important step in order to guarantee the highest quality and reproducibility of genetic test results