Complete Genome Sequence of a Sucrose-Nonfermenting Epidemic Strain of Vibrio cholerae O1 from Brazil

Submitted by Sandra Infurna ([email protected]) on 2018-11-29T16:27:51Z No. of bitstreams: 1 anaCP_vicente_etal_IOC_2012.pdf: 85091 bytes, checksum: 21a9ac0bb61adafc66c73f4f8f851d58 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2018-11-29T16:37:43Z (GMT) No. of bitstreams: 1 anaCP_vicente_etal_IOC_2012.pdf: 85091 bytes, checksum: 21a9ac0bb61adafc66c73f4f8f851d58 (MD5)Made available in DSpace on 2018-11-29T16:37:43Z (GMT). No. of bitstreams: 1 anaCP_vicente_etal_IOC_2012.pdf: 85091 bytes, checksum: 21a9ac0bb61adafc66c73f4f8f851d58 (MD5) Previous issue date: 2012Instituto Evandro Chagas. Laboratório de Microbiologia Ambiental. Ananindeua, PA, Brasil.Instituto Evandro Chagas. Laboratório de Microbiologia Ambiental. Ananindeua, PA, Brasil.Instituto Evandro Chagas. Secção de Bacteriologia. Ananindeua, PA, Brasil.Instituto Evandro Chagas. Centro de Inovação Tecnológica. Ananindeua, PA, Brasil.Instituto Evandro Chagas. Centro de Inovação Tecnológica. Ananindeua, PA, Brasil.Instituto Evandro Chagas. Centro de Inovação Tecnológica. Ananindeua, PA, Brasil.Instituto Evandro Chagas. Centro de Inovação Tecnológica. Ananindeua, PA, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microrganismos. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microrganismos. Rio de Janeiro, RJ. Brasil.Instituto Evandro Chagas. Laboratório de Microbiologia Ambiental. Ananindeua, PA, Brasil.We report the genome sequence of Vibrio cholerae strain IEC224, which fails to ferment sucrose. It was isolated from a cholera outbreak in the Amazon. The defective sucrose phenotype was determined to be due to a frameshift mutation, and a molecular marker of the Latin American main epidemic lineage was identified

Analysis of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) for yellow fever diagnostic

This study was partially supported by CNPq (Conselho Nacional para o Desenvolvimento Científico e Tecnológico) projects 401558/2013-4; 457664/2013-4, 486069/2012-5 and 301641/2010-2), and CNPq/CAPES/FAPESPA (project 573739-2008-0).Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovações Tecnológicas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovações Tecnológicas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovações Tecnológicas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovações Tecnológicas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovações Tecnológicas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil / University of Para State. Department of Pathology. Belem, PA, Brazil.University of Texas Medical Branch. Department of Pathology. Galveston, TX, USA.University of Texas Medical Branch. Department of Pathology. Galveston, TX, USA.Yellow Fever virus (YFV) is an important human pathogen in tropical areas of Africa and South America. Although an efficient vaccine is available and has been used since the early 1940s, sylvatic YFV transmission still occurs in forested areas where anthropogenic actions are present, such as mineral extraction, rearing livestock and agriculture, and ecological tourism. In this context, two distinct techniques based on the RT-PCR derived method have been previously developed, however both methods are expensive due to the use of thermo cyclers and labeled probes. We developed isothermal genome amplification, which is a rapid, sensitive, specific and low cost molecular approach for YFV genome detection. This assay used a set of degenerate primers designed for the NS1 gene and was able to amplify, within 30 min in isothermal conditions, the YFV 17D vaccine strain derived from an African wild prototype strain (Asibi),as well as field strains from Brazil, other endemic countries from South and Central America, and the Caribbean. The generic RT-LAMP assay could be helpful for YFV surveillance in field and rapid response during outbreaks in endemic areas

Phylogeography of dengue virus serotype 4, Brazil, 2010-2011.

Dengue virus serotype 4 (DENV-4) reemerged in Roraima State, Brazil, 28 years after it was last detected in the country in 1982. To study the origin and evolution of this reemergence, full-length sequences were obtained for 16 DENV-4 isolates from northern (Roraima, Amazonas, Pará States) and northeastern (Bahia State) Brazil during the 2010 and 2011 dengue virus seasons and for an isolate from the 1982 epidemic in Roraima. Spatiotemporal dynamics of DENV-4 introductions in Brazil were applied to envelope genes and full genomes by using Bayesian phylogeographic analyses. An introduction of genotype I into Brazil from Southeast Asia was confirmed, and full genome phylogeographic analyses revealed multiple introductions of DENV-4 genotype II in Brazil, providing evidence for >3 introductions of this genotype within the last decade: 2 from Venezuela to Roraima and 1 from Colombia to Amazonas. The phylogeographic analysis of full genome data has demonstrated the origins of DENV-4 throughout Brazil

Phylogeography of dengue virus serotype 4, Brazil, 2010-2011

Dengue virus serotype 4 (DENV-4) reemerged in Roraima State, Brazil, 28 years after it was last detected in the country in 1982. To study the origin and evolution of this reemergence, full-length sequences were obtained for 16 DENV-4 isolates from northern (Roraima, Amazonas, Pará States) and northeastern (Bahia State) Brazil during the 2010 and 2011 dengue virus seasons and for an isolate from the 1982 epidemic in Roraima. Spatiotemporal dynamics of DENV-4 introductions in Brazil were applied to envelope genes and full genomes by using Bayesian phylogeographic analyses. An introduction of genotype I into Brazil from Southeast Asia was confirmed, and full genome phylogeographic analyses revealed multiple introductions of DENV-4 genotype II in Brazil, providing evidence for >3 introductions of this genotype within the last decade: 2 from Venezuela to Roraima and 1 from Colombia to Amazonas. The phylogeographic analysis of full genome data has demonstrated the origins of DENV-4 throughout Brazil.status: publishe

Genome of the Latin American epidemic <i>Vibrio cholerae</i> marker phage.

<p>Graphical representation of the genes that correspond to the genome of a bacteriophage that is present in all the Latin American epidemic strains tested in this study. The CDS are the blue arrows that are pointed towards the direction they are coded in the genome. The putative protein functions are listed below, with a corresponding number to its localization in the image. (Images generated in the Geneious software – reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037283#pone.0037283-Drummond1" target="_blank">[24]</a>)</p

General genome features of the <i>V. cholerae</i> strain IEC224.

<p>General genome features of the <i>V. cholerae</i> strain IEC224.</p

The altered sucrose phenotype of the strain IEC224 is due to a frame-shift mutation.

<p>The characteristic phenotype of <i>Vibrio cholerae</i> is to produce shiny gold colonies after 48 h incubation on TCBS agar (as pictured on the right side). The strain IEC224 fails to ferment sucrose and colonies remain green (pictured on the left). The only genomic difference between a functioning sucrose fermenter and the IEC224 strain is an insertion in the gene coding for the sucrose-specific IIB domain of the PTS system, which is shown above in the aligned fragments of the mutated IEC224 gene and the functioning N16961 gene. A diagram with the metabolic role of this protein is illustrated in the center, showing that it is a carrier that selectively transports sucrose into the cell and phosphorylates it to signal downstream reactions. A model of the functioning protein structure is shown on the top left, as well as a model for the altered structure can be seen in the top right. (Model generated by PHYRE², following the pipeline of reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037283#pone.0037283-Kelley1" target="_blank">[25]</a>)</p

Variants of the Latin American epidemic phage in sequenced V. cholerae genomes.

<p>The assembly of sequencing reads from 16 other El Tor <i>V. cholerae</i> genomes from Latin America, and their putative ancestor strain from Angola, revealed the presence of the Latin American epidemic phage in all strains. The genomic variations were in 8 sites numbered from bases 0 through 49,291 (right). Collectively these strains formed 10 variants of the phage, with the variant A being the most abundant. This variant is shared with the putative ancestor strain. All strains accumulated at least one SNP after 1992.</p