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Complete genome sequence of Mycobacterium chelonae type strain CCUG 47445, a rapidly growing species of nontuberculous mycobacteria

Mycobacterium chelonae strains are ubiquitous rapidly growing mycobacteria associated with skin and soft tissue infections, cellulitis, abscesses, osteomyelitis, catheter infections, disseminated diseases, and postsurgical infections after implants with prostheses, transplants, and even hemodialysis procedures. Here, we report the complete genome sequence of M. chelonae type strain CCUG 47445.This work, including the efforts of Antoni Bennasar-Figueras, was funded by Ministerio de Economía y Competitividad (MINECO) (CGL2012-39604).Peer Reviewe

Rapid identification of Salmonella typhimurium, S. enteritidis and S. virchow isolates by Polymerase Chain Reaction based fingerprinting methods

In this study we used and evaluated three rapid molecular typing methods for the identification of three frequent, clinically significant Salmonella serovars on the basis of the ease, simplicity and reproducibility of the chosen methods. We determined the genetic diversity among several isolates of Salmonella enteritidis, S. typhimurium and S. virchow, and compared them with other enterobacteria by using the repetitive extragenic palindromic (REP) sequences, the enterobacterial repetitive intergenic consensus (ERIC) sequences, and the 16S–23S rDNA intergenic spacer region (ITS1). The objective was to evaluate their potential application to discriminate among members of the species Salmonella enterica subspecies enterica using the genetic diversity of the group found by genomic fingerprinting. The three different serovars of Salmonella studied gave reproducible and distinguishable profiles using whichever of the above mentioned polymerase chain reaction (PCR) methods assayed. The conserved patterns in each serovar allowed for easy differentiation from other serovars of Salmonella

PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species

<p>Abstract</p> <p>Background</p> <p>The genus <it>Pseudomonas </it>comprises more than 100 species of environmental, clinical, agricultural, and biotechnological interest. Although, the recommended method for discriminating bacterial species is DNA-DNA hybridisation, alternative techniques based on multigenic sequence analysis are becoming a common practice in bacterial species discrimination studies. Since there is not a general criterion for determining which genes are more useful for species resolution; the number of strains and genes analysed is increasing continuously. As a result, sequences of different genes are dispersed throughout several databases. This sequence information needs to be collected in a common database, in order to be useful for future identification-based projects.</p> <p>Description</p> <p>The PseudoMLSA Database is a comprehensive database of multiple gene sequences from strains of <it>Pseudomonas </it>species. The core of the database is composed of selected gene sequences from all <it>Pseudomonas </it>type strains validly assigned to the genus through 2008. The database is aimed to be useful for MultiLocus Sequence Analysis (MLSA) procedures, for the identification and characterisation of any <it>Pseudomonas </it>bacterial isolate. The sequences are available for download via a direct connection to the National Center for Biotechnology Information (NCBI). Additionally, the database includes an online BLAST interface for flexible nucleotide queries and similarity searches with the user's datasets, and provides a user-friendly output for easily parsing, navigating, and analysing BLAST results.</p> <p>Conclusions</p> <p>The PseudoMLSA database amasses strains and sequence information of validly described <it>Pseudomonas </it>species, and allows free querying of the database via a user-friendly, web-based interface available at <url>http://www.uib.es/microbiologiaBD/Welcome.html</url>. The web-based platform enables easy retrieval at strain or gene sequence information level; including references to published peer-reviewed articles, and direct external links to more specialized strain information databases (StrainInfo) and GeneBank (NCBI). The PseudoMLSA is intended to provide helpful strain-sequence information for a better and more comprehensive discriminative multigenic sequence based analysis of this special group of bacteria, contributing to enhance our understanding of the evolution of <it>Pseudomonas </it>species.</p

Phylogenomics and systematics in Pseudomonas

© 2015 Gomila, Peña, Mulet, Lalucat and García-Valdés. The genus Pseudomonas currently contains 144 species, making it the genus of Gram-negative bacteria that contains the largest number of species. Currently, multilocus sequence analysis (MLSA) is the preferred method for establishing the phylogeny between species and genera. Four partial gene sequences of housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) were obtained from 112 complete or draft genomes of strains related to the genus Pseudomonas that were available in databases. These genes were analyzed together with the corresponding sequences of 133 Pseudomonas type strains of validly published species to assess their correct phylogenetic assignations. We confirmed that 30% of the sequenced genomes of non-type strains were not correctly assigned at the species level in the accepted taxonomy of the genus and that 20% of the strains were not identified at the species level. Most of these strains had been isolated and classified several years ago, and their taxonomic status has not been updated by modern techniques. MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC). TETRA was useful for discriminating Pseudomonas from other genera, whereas ANIb and GGDC clearly separated strains of different species. ANIb showed the strongest correlation with MLSA. The correct species classification is a prerequisite for most diversity and evolutionary studies. This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.Financial support was obtained from the Spanish MINECO through projects CGL2011-24318 and Consolider CSD2009-00006, as well as funds for competitive research groups from the Government of the Balearic Islands (the last two funds with FEDER cofunding). MG and AP were supported by a postdoctoral contract from the University of the Balearic IslandsPeer Reviewe

The World Health Organization Short Disability Assessment Schedule: a validation study in patiens with schizophrenia

Purpose: The World Health Organization Short Disability Assessment Schedule (DAS-s) is used for patients with schizophrenia even though no validation is available. This paper addresses this issue by dealing with its psychometric properties in a clinical sample of patients with schizophrenia. Methods: Two hundred forty-one patients from 10 Adult Mental Health Care Centres (AMHCC) meeting the following inclusion criteria were included: 1) International Classification of Diseases-10 or ICD-10 diagnosis o schizophrenia; 2) Global Assessment of Functioning scores or GAF ≤50; 3) Illness duration of more than 2 years; and 4) Clinical stability at assessment time. Patients were evaluated at baseline and at one-year follow-up regarding disability, socio-demographic and clinical variables, psychosocial measures and use of mental health services. Results: The factor analysis revealed a single factor that explained 60.57% of the variance. Internal consistency values were appropriate for the DAS-s total (0.78 at baseline and 0.78 at one year follow-up). Correlations between DAS-s scores and those of global functioning, psychiatric symptoms, social support and quality of life ranged between small and moderate (range: 0.13-0.39). There were significant differences between groups of patients with schizophrenia in the DAS-s. Patients who were unemployed, with lower global functioning, with cognitive impairment and lacking social support scored significantly lower in DAS-s scores. After one year follow-up, there was a non-significant decrease in DAS-s scores and patients improved significantly in overall functioning and psychiatric symptoms. Discussion: This study shows that the DAS-s has good reliability and validity, and suggests that it is suitable for the assessment of disability in patients with schizophrenia

Revisión de intervenciones psicoterapéuticas para personas con esquizofrenia

In recent years, various clinical practice guidelines have been developed for people with schizophrenia recommending different psychotherapeutic interventions. The objective of this study is to identify, review and compare the recommendations in these guidelines on the efficacy of psychotherapeutic interventions in schizophrenia. We conducted a computerized search of the main clinical practice guideline developers and repositories, identifying five different clinical practice guidelines. We extracted descriptive information from each and compared their recommendations on the efficacy of psychotherapeutic interventions. They were evidence-based consensus guidelines developed by multidisciplinary groups. Family intervention, cognitive behavioural therapy (CBT), social skills training, arts therapies, cognitive rehabilitation, psychoeducation, psychodynamic psychotherapy and counselling were recommended in the identified guidelines. There was strong consensus on the efficacy of CBT and family intervention and high-quality evidence supporting their use. When choosing psychotherapeutic interventions for people with schizophrenia, it is recommended that mental health professionals take clinical practice guidelines into account as well as the setting in which they are being applied, since implementation of health-care interventions is associated with the characteristics of the service system. Schizophrenia treatment should include biological, psychosocial and community interventionsEn los últimos años han aparecido varias guías de práctica clínica para personas con esquizofrenia que recomiendan diversas intervenciones psicoterapéuticas. El objetivo de este estudio es identificar, revisar y comparar las recomendaciones sobre la eficacia de las intervenciones psicoterapéuticas en la esquizofrenia de estas guías. Se realizó una búsqueda electrónica sobre la esquizofrenia en los principales elaboradores y repositorios de guías de práctica clínica. Se identificaron cinco guías de práctica clínica. Se extrajeron datos descriptivos de cada una y se compararon sus recomendaciones sobre las intervenciones psicoterapéuticas. Las guías fueron desarrolladas por grupos multidisciplinarios, consensuadas y se basaban en la evidencia. El arte terapia, la terapia cognitivo-conductual (TCC), la rehabilitación cognitiva, el asesoramiento, la intervención familiar, la psicoterapia psicodinámica, la psicoeducación y entrenamiento en habilidades sociales se recomendaban en las guías identificadas. Hubo un alto consenso sobre la eficacia de la TCC y de la intervención familiar, así como evidencias de alta calidad que apoyaban su uso. Al elegir intervenciones psicoterapéuticas para personas con esquizofrenia, se recomienda que los profesionales de la salud mental tengan en cuenta las guías de práctica clínica y el contexto en el que se ofrecerán ya que las características del sistema están asociadas a la implementación de estas intervenciones. El tratamiento de la esquizofrenia debe incluir intervenciones biológicas, psicosociales y comunitaria

Considering variables for the assignment of patients with schizophrenia to a case management programme

The elements and intensity of Case Management (CM) practices should be established according to patients' needs. Therefore, it is important to improve the knowledge of the needs of patients in such a community-based intervention. This paper deals with this issue by characterizing two groups of patients receiving CM or a Standard Treatment Programme (STP) and identifying the patients' characteristics associated with the provision of CM services. We recruited 241 patients with schizophrenia from 10 Adult Mental Health Centers from Barcelona (Catalonia, Spain). We analyzed the profile of new patients included in a clinical and non-intensive CM program with that of patients in a STP. CM patients showed a poorer profile. Community psychiatric visits, social services, education, physical health, needs and positive symptoms were significantly associated with the provision of CM services. This study may help in identifying patients' necessities and strengthen the CM programme

Validation of the modified DUKE-UNC functional social support questionnaire in patients with schizophrenia

Abstract Purpose: The modified DUKE-UNC Functional Social Support Questionnaire (FSSQ) is considered an assessment tool for patients with schizophrenia. However, it has not been validated in this patient population. This issue is addressed here by examining the tool's psychometric properties in a clinical sample of patients with schizophrenia. Methods: Two hundred and forty-one patients from 10 Adult Mental Health Centres (AMHC) meeting the following inclusion criteria were included: 1) International Classification of Diseases-10 (ICD-10) diagnosis of schizophrenia; 2) Global Assessment of Functioning (GAF) scores ≤50; 3) Illness duration of more than 2 years; and 4) Clinical stability. Patients were evaluated at baseline and at one-year follow-up for clinical and psychosocial variables. Results: The factor analysis revealed two factors that explained 54.15% of the variance. Internal consistency was excellent for the total FSSQ (0.87 at baseline and 0.88 at one year follow-up) and ranged between adeq uate and excellent for FSSQ domains. Correlations between FSSQ scores and those of global functioning, psychiatric symptoms, disability and quality of life ranged between small and large. There were significant differences between groups of patients with schizophrenia in FSSQ scores. Patients with higher levels of somatic complaints and patients who were disabled scored significantly lower in some or all FSSQ scores. After one-year follow-up, patients improved in overall functioning and there was a decrease in psychiatric symptoms. Conclusions: The FSSQ is a reliable and valid instrument for the assessment of perceived social support in patients with schizophrenia

Revisión de intervenciones psicoterapéuticas para personas con esquizofrenia

In recent years, various clinical practice guidelines have been developed for people with schizophrenia recommending different psychotherapeutic interventions. The objective of this study is to identify, review and compare the recommendations in these guidelines on the efficacy of psychotherapeutic interventions in schizophrenia. We conducted a computerized search of the main clinical practice guideline developers and repositories, identifying five different clinical practice guidelines. We extracted descriptive information from each and compared their recommendations on the efficacy of psychotherapeutic interventions. They were evidence-based consensus guidelines developed by multidisciplinary groups. Family intervention, cognitive behavioural therapy (CBT), social skills training, arts therapies, cognitive rehabilitation, psychoeducation, psychodynamic psychotherapy and counselling were recommended in the identified guidelines. There was strong consensus on the efficacy of CBT and family intervention and high-quality evidence supporting their use. When choosing psychotherapeutic interventions for people with schizophrenia, it is recommended that mental health professionals take clinical practice guidelines into account as well as the setting in which they are being applied, since implementation of health-care interventions is associated with the characteristics of the service system. Schizophrenia treatment should include biological, psychosocial and community interventionsEn los últimos años han aparecido varias guías de práctica clínica para personas con esquizofrenia que recomiendan diversas intervenciones psicoterapéuticas. El objetivo de este estudio es identificar, revisar y comparar las recomendaciones sobre la eficacia de las intervenciones psicoterapéuticas en la esquizofrenia de estas guías. Se realizó una búsqueda electrónica sobre la esquizofrenia en los principales elaboradores y repositorios de guías de práctica clínica. Se identificaron cinco guías de práctica clínica. Se extrajeron datos descriptivos de cada una y se compararon sus recomendaciones sobre las intervenciones psicoterapéuticas. Las guías fueron desarrolladas por grupos multidisciplinarios, consensuadas y se basaban en la evidencia. El arte terapia, la terapia cognitivo-conductual (TCC), la rehabilitación cognitiva, el asesoramiento, la intervención familiar, la psicoterapia psicodinámica, la psicoeducación y entrenamiento en habilidades sociales se recomendaban en las guías identificadas. Hubo un alto consenso sobre la eficacia de la TCC y de la intervención familiar, así como evidencias de alta calidad que apoyaban su uso. Al elegir intervenciones psicoterapéuticas para personas con esquizofrenia, se recomienda que los profesionales de la salud mental tengan en cuenta las guías de práctica clínica y el contexto en el que se ofrecerán ya que las características del sistema están asociadas a la implementación de estas intervenciones. El tratamiento de la esquizofrenia debe incluir intervenciones biológicas, psicosociales y comunitaria