Navegando por Autor "GUARALDI, Ana Luiza de Mattos"

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Acesso aberto (Open Access)
Draft genome sequences of two species of “difficult-to-identify” human-pathogenic corynebacteria: implications for better identification tests.
(Ivyspring International Publisher, 2015) PACHECO, Luis Gustavo Carvalho; GUARALDI, Ana Luiza de Mattos; SANTOS, Carolina Silva; VERAS, Adonney Allan de Oliveira; GUIMARÃES, Luís Carlos; ABREU, Vinicius Augusto Carvalho de; PEREIRA, Felipe Luiz; SOARES, Siomar de Castro; DORELLA, Fernanda Alves; CARVALHO, Alex Fiorini de; LEAL, Carlos Augusto Gomes; FIGUEIREDO, Henrique Cesar Pereira; RAMOS, Juliana Nunes; VIEIRA, Verônica Viana; FARFOUR, Eric; GUISO, Nicole; HIRATA JÚNIOR, Raphael; AZEVEDO, Vasco Ariston de Carvalho; SILVA, Artur Luiz da Costa da; RAMOS, Rommel Thiago Juca
Non-diphtheriae Corynebacterium species have been increasingly recognized as the causative agents of infections in humans. Differential identification of these bacteria in the clinical microbiology laboratory by the most commonly used biochemical tests is challenging, and normally requires additional molecular methods. Herein, we present the annotated draft genome sequences of two isolates of “difficult-to-identify” human-pathogenic corynebacterial species: C. xerosis and C. minutissimum. The genome sequences of ca. 2.7 Mbp, with a mean number of 2,580 protein en coding genes, were also compared with the publicly available genome sequences of strains of C. amycolatum and C. striatum. These results will aid the exploration of novel biochemical reactions to improve existing identification tests as well as the development of more accurate molecular identification methods through detection of species-specific target genes for isolate’s identification or drug susceptibility profiling.
Acesso aberto (Open Access)
PIPS: Pathogenicity Island Prediction Software
(Public Library of Science, 2012-02) SOARES, Siomar de Castro; ABREU, Vinicius Augusto Carvalho de; RAMOS, Rommel Thiago Juca; CERDEIRA, Louise Teixeira; SILVA, Artur Luiz da Costa da; BAUMBACH, Jan; TROST, Eva; TAUCH, Andreas; HIRATA JÚNIOR, Raphael; GUARALDI, Ana Luiza de Mattos; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho
The adaptability of pathogenic bacteria to hosts is influenced by the genomic plasticity of the bacteria, which can be increased by such mechanisms as horizontal gene transfer. Pathogenicity islands play a major role in this type of gene transfer because they are large, horizontally acquired regions that harbor clusters of virulence genes that mediate the adhesion, colonization, invasion, immune system evasion, and toxigenic properties of the acceptor organism. Currently, pathogenicity islands are mainly identified in silico based on various characteristic features: (1) deviations in codon usage, G+C content or dinucleotide frequency and (2) insertion sequences and/or tRNA genetic flanking regions together with transposase coding genes. Several computational techniques for identifying pathogenicity islands exist. However, most of these techniques are only directed at the detection of horizontally transferred genes and/or the absence of certain genomic regions of the pathogenic bacterium in closely related non-pathogenic species. Here, we present a novel software suite designed for the prediction of pathogenicity islands (pathogenicity island prediction software, or PIPS). In contrast to other existing tools, our approach is capable of utilizing multiple features for pathogenicity island detection in an integrative manner. We show that PIPS provides better accuracy than other available software packages. As an example, we used PIPS to study the veterinary pathogen Corynebacterium pseudotuberculosis, in which we identified seven putative pathogenicity islands.
Acesso aberto (Open Access)
Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
(Dove Medical Press, 2012-02) FERREIRA, Vívian D'Afonseca da Silva; SOARES, Siomar de Castro; ALI, Amjad; SANTOS, Anderson Rodrigues dos; GOMIDE, Anne Cybelle Pinto; ROCHA, Aryane Aparecida Magalhães Cassiano; FARIA, Cássio de Jesus; BARBOSA, Eudes Guilherme Vieira; GUIMARÃES, Luís Carlos; ESLABÃO, Marcus Redü; ALMEIDA, Sintia Silva de; ABREU, Vinicius Augusto Carvalho de; ZERLOTINI NETO, Adhemar; CARNEIRO, Adriana Ribeiro; CERDEIRA, Louise Teixeira; RAMOS, Rommel Thiago Juca; HIRATA JÚNIOR, Raphael; GUARALDI, Ana Luiza de Mattos; TROST, Eva; TAUCH, Andreas; SILVA, Artur Luiz da Costa da; SCHNEIDER, Maria Paula Cruz; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho
Background: The reannotation of genomes already on file is a new approach to discovering new genetic elements and to make the genomes more descriptive and current with relevant features regarding the organism’s lifestyle. Within this approach, the present study aimed to reannotate the genome of the Gram-positive human pathogen Corynebacterium diphtheriae, which causes diphtheria. The deposit of massive amounts of information linked to other spe cies of the genus Corynebacterium has facilitated the updating of the genomic interpretation of this microorganism. Additionally, the emergence of invasive disease by nontoxigenic strains of C. diphtheriae and the reemergence of diphtheria in partially immunized populations have given impetus to new studies in relation to its structural and functional genome. Results: In relation to structural genomics, 23 coding regions (coding sequences) were deleted and 71 new genes were added to the genome annotation. Nevertheless, all the pseudogenes were validated and ten new pseudogenes were created. In relation to functional genomics, about 57% of the genome annotation was updated and became functionally more informative. The product descriptions of 41% (973 proteins) were updated. Among them, 370 that were previously annotated as “hypothetical proteins,” now have more informative descriptions. With the new annotation, the plasticity of the genome became evident, which shows improvements in the annotation of 13 pathogenicity islands already described in the literature. In addition, the large number of transposases and the presence of structural genes of bacteriophages make their genomic versatility evident. Contrasting with this reality, it also allowed the clarification of some aspects concerned with mechanisms used by C. diphtheriae to stop the invasion of the genome by bacteriophages, mediated by the clustered regularly interspaced short palindromic repeats region. Conclusion: The reannotation of the C. diphtheriae genome provided an improvement in annotation of the C. diphtheriae genome in several aspects, such as virulence characteristics and plasticity events. Moreover, the protocol used here can be extended to various other pathogens in order to improve the genomic information already on file in public databases and to minimize propagating errors. The reannotated archive and updated archive are available at: http://lgcm. icb.ufmg.br/pub/C_diphtheriae_reannotation.embl.