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

Pseudomonas entomophila: A Versatile Bacterium with Entomopathogenic Properties

Pseudomonas entomophila is unique among Pseudomonas species in being able to activate a systemic immune response in both Drosophila larvae and adults. It has been subsequently shown that oral infections with high doses of this bacterium are highly pathogenic to Drosophila and cause massive destruction of the Drosophila gut epithelium. Besides Drosophila, P. entomophila was able to kill other insects from at least three different orders, suggesting that it has a potentially wide host range and making it a promising model for the study of host pathogen interactions and for the development of bio-control agents against insect pests. In order to unravel the features contributing to P. entomophila’s pathogenic properties, its complete genome was sequenced and genetic screens were performed to identify virulence factors encoded by this bacterium. The aim of this chapter is to review the current knowledge we have on this bacterium with a particular focus on the pathogenesis it induces, its virulence effectors and their genetic regulatio

Respiratory infection by Corynebacterium striatum: Epidemiological and clinical determinants

© 2014 The Authors. The increasing prevalence of advanced chronic respiratory disease, with frequent exposure to broad-spectrum antibiotics for repeated and prolonged hospitalizations, favours the emergence of nosocomial respiratory infection by Gram-positive bacteria, such as outbreaks of Corynebacterium striatum. There is little evidence about patterns of respiratory infection, transmission and adaptive ability of this pathogen. Seventy-two C. striatum isolates from 51 advanced respiratory patients, mainly chronic obstructive pulmonary disease, were studied during 38 months. Patients were 74.8 ± 8.6 years old and 81.9% were men, who had required an average of 2.2 hospitalizations and 63.5 days in the hospital in the previous year. Of 49 isolates from 42 patients we were able to identify 12 clones by multilocus sequence analysis (MLSA), nine phenotypic variants and 22 antibiotic susceptibility patterns, and we determined their clinical and epidemiological determinants. MLSA allows identification of the existence of nosocomial outbreaks by transmission of the same or different clones, the persistence of the same clone in the environment or in patient airways for months. The study showed the high variability and adaptive capacity of the isolates, the antibiotic multidrug-resistance in all of them, and their contribution to a high morbidity and mortality (41%) during the study period.This work was supported by the General Board for Research, Technological Development and Innovation of the Department of Finance and Innovation of the Autonomous Community of the Balearic Islands (Direcció General de Recerca, Desenvolupament Tecnològic i Innovació, de la Conselleria d'Hisenda i Innovació, de la Comunitat Autònoma de les Illes Balears). This work was supported also by funding from Spanish MINECO through Consolider CSD2009-00006. Margarita Gomila was supported by a postdoctoral contract from the University of the Balearic Islands, with funds from the Spanish Ministry of Education, Culture and Sports through the International Excellence Campus ProgrammePeer Reviewe

Identification and diversity of multiresistant Corynebacterium striatum clinical isolates by MALDI-TOF mass spectrometry and by a multigene sequencing approach

<p>Abstract</p> <p>Background</p> <p>The genus <it>Corynebacterium </it>is composed of Gram-positive bacteria that are widely distributed throughout the environment; these bacteria are also part of the normal microbiota of human skin and mucous membranes. Multiple studies have shown that species of this genus, including <it>C. striatum</it>, become pathogenic to humans under special conditions. Our aim was to determine the characteristics of clinical multiresistant strains of <it>C. striatum </it>that were isolated in our geographical region, to determine their diversity, and to compare them with the type strain and with related species. We studied fifty-two strains of <it>C. striatum </it>isolated from different hospitals from Mallorca, Spain, mainly from the Hospital Joan March in Bunyola, Mallorca. Most of the strains were isolated from sputum cultures of respiratory samples from patients with chronic obstructive pulmonary disease. To gain further insight into the genetic diversity of the strains, we analysed several housekeeping genes and other genes associated with antibiotic resistance. Strains were also characterised phenotypically by their antibiotic resistance profiles and by MALDI-TOF mass spectrometry analysis.</p> <p>Results</p> <p>The ITS1 region, <it>gyrA </it>and <it>rpoB </it>were chosen as the appropriate genes in the <it>C. striatum </it>genome to study the genetic diversity of <it>C. striatum </it>species and to discriminate between strains. After analysing these three genes, four sequence types (ST2, ST4, ST1 and ST11) were found to be the most abundant. Splits tree analysis of the strains demonstrated that these clinical isolates did not share any alleles with the type strain of the species. Recombination was detected within all of the <it>C. striatum </it>isolates, and different clonal populations were detected within the samples.</p> <p>Conclusions</p> <p>Our results demonstrate that the isolates were best identified using gene-based molecular methods; using these methods, the isolated strains were determined to be different from the type strain of <it>C. striatum</it>. The ITS1 region and the <it>gyrA </it>and <it>rpoB </it>genes were selected because of their variability and were the most useful tools for discriminating between strains. The phenotype and antibiotype characteristics of the strains did not seem suitable for typing purposes. MALDI-TOF mass spectrometry can be a useful method for identifying and discriminating between <it>C. striatum </it>strains.</p

IS Pst9, an ISL3-like insertion sequence from Pseudomonas stutzeri AN10 involved in catabolic gene inactivation

A novel insertion sequence (IS), ISPst9, from Pseudomonas stutzeri AN10 was cloned and characterized. ISPst9 is a typical bacterial IS, consisting of a 2472-bp element flanked by 24-bp perfect inverted repeats that generates 8-bp AT-rich target duplications upon insertion. The sequence also contains a gene that encodes an active transposase (TnpA) with significant amino acid identity to members of the ISL3 family. Southern blot analysis of digested genomic DNA of strain AN10 and its 4-chlorosalicylate-degrading derivative strain AN142 demonstrated that native ISPst9 transposes in multiple copies, with one of them responsible for the nahH insertional inactivation observed in strain AN142. Precise excision of ISPst9 yielded NahH+ revertants of AN142 at high frequencies (up to 10-6). In vivo transposition, mainly in multiple copies, of an ISPst9 derivative containing a KmR cassette cloned into a suicide vector was also demonstrated. Hybridization experiments carried out with different strains of P. stutzeri and with 292 phylogenetically distinct environmental isolates suggested that the presence of an ISPst9-like IS occurs in diverse bacteria together with the presence of aromatic hydrocarbon-degrading determinants

Draft genome sequence of Pseudomonas stutzeri strain B1SMN1, a nitrogen-fixing and naphthalene-degrading strain isolated from wastewater

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ISPst9, an ISL3-like insertion sequence from Pseudomonas stutzeri AN10 involved in catabolic gene inactivation

A novel insertion sequence (IS), ISPst9, from Pseudomonas stutzeri AN10 was cloned and characterized. ISPst9 is a typical bacterial IS, consisting of a 2472-bp element flanked by 24-bp perfect inverted repeats that generates 8-bp AT-rich target duplications upon insertion. The sequence also contains a gene that encodes an active transposase (TnpA) with significant amino acid identity to members of the ISL3 family. Southern blot analysis of digested genomic DNA of strain AN 10 and its 4-chlorosalicylate-degrading derivative strain AN142 demonstrated that native ISPst9 transposes in multiple copies, with one of them responsible for the nahH insertional inactivation observed in strain AN142. Precise excision of ISPst9 yielded NahH+ revertants of AN142 at high frequencies (up to 10-6). In vivo transposition, mainly in multiple copies, of an ISPst9 derivative containing a KmR cassette cloned into a suicide vector was also demonstrated. Hybridization experiments carried out with different strains of P. stutzeri and with 292 phylogenetically distinct environmental isolates suggested that the presence of an ISPst9-like IS occurs in diverse bacteria together with the presence of aromatic hydrocarbon-degrading determinants (Journal)Funds were obtained from projects VEM2003-20565 and CTM2005-01783 from MEC, and project PRIB2004-10152 from CAIBPeer Reviewe