Navegando por Autor "BARH, Debmalya"

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Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by rapid next generation sequencing technology
(BioMed Central, 2012) HASSAN, Syed Shah; GUIMARÃES, Luís Carlos; PEREIRA, Ulisses de Pádua; ISLAM, Arshad; ALI, Amjad; BAKHTIAR, Syeda Marriam; RIBEIRO, Dayana; SANTOS, Anderson Rodrigues dos; SOARES, Siomar de Castro; DORELLA, Fernanda Alves; GOMIDE, Anne Cybelle Pinto; SCHNEIDER, Maria Paula Cruz; BARBOSA, Maria Silvanira Ribeiro; ALMEIDA, Sintia Silva de; ABREU, Vinicius Augusto Carvalho de; ABURJAILE, Flavia Figueira; CARNEIRO, Adriana Ribeiro; CERDEIRA, Louise Teixeira; NASCIMENTO, Karina Kelly Fiaux do; BARBOSA, Eudes Guilherme Vieira; DINIZ, Carlos Augusto Almeida; ROCHA, Flávia de Souza; RAMOS, Rommel Thiago Juca; JAIN, Neha; TIWARI, Sandeep; BARH, Debmalya; MIYOSHI, Anderson; MÜLLER, Borna; SILVA, Artur Luiz da Costa da; AZEVEDO, Vasco Ariston de Carvalho
The Actinobacteria, Corynebacterium pseudotuberculosis strain P54B96, a nonmotile, non sporulating and a mesophile bacterium, was isolated from liver, lung and mediastinal lymph node lesions in an antelope from South Africa. This strain is interesting in the sense that it has been found together with non-tuberculous mycobacteria (NTMs) which could nevertheless play a role in the lesion formation. In this work, we describe a set of features of C. pseudotuberculosis P54B96, together with the details of the complete genome sequence and annotation. The genome comprises of 2.34 Mbp long, single circular genome with 2,084 protein-coding genes, 12 rRNA, 49 tRNA and 62 pseudogenes and a G+C content of 52.19%. The analysis of the genome se quence provides means to better understanding the molecular and genetic basis of virulence of this bacterium, enabling a detailed investigation of its pathogenesis.
Acesso aberto (Open Access)
Exoproteome and Secretome Derived Broad Spectrum Novel Drug and Vaccine Candidates in Vibrio cholerae Targeted by Piper betel Derived Compounds
(Public Library of Science, 2013-01) BARH, Debmalya; SHARMA, Neha Barve; GUPTA, Krishnakant; CHANDRA, Sudha; JAIN, Neha; TIWARI, Sandeep; LEON-SICAIROS, Nidia; CANIZALEZ-ROMAN, Adrian; SANTOS, Anderson Rodrigues dos; HASSAN, Syed Shah; ALMEIDA, Sintia Silva de; RAMOS, Rommel Thiago Juca; ABREU, Vinicius Augusto Carvalho de; CARNEIRO, Adriana Ribeiro; SOARES, Siomar de Castro; CASTRO, Thiago Luiz de Paula; MIYOSHI, Anderson; SILVA, Artur Luiz da Costa da; KUMAR, Anil; NARAYAN MISRA, Amarendra; BLUM, Kenneth; BRAVERMAN, Eric R.; AZEVEDO, Vasco Ariston de Carvalho
Vibrio cholerae is the causal organism of the cholera epidemic, which is mostly prevalent in developing and underdeveloped countries. However, incidences of cholera in developed countries are also alarming. Because of the emergence of new drug resistant strains, even though several generic drugs and vaccines have been developed over time, Vibrio infections remain a global health problem that appeals for the development of novel drugs and vaccines against the pathogen. Here, applying comparative proteomic and reverse vaccinology approaches to the exoproteome and secretome of the pathogen, we have identified three candidate targets (ompU, uppP and yajC) for most of the pathogenic Vibrio strains. Two targets (uppP and yajC) are novel to Vibrio, and two targets (uppP and ompU) can be used to develop both drugs and vaccines (dual targets) against broad spectrum Vibrio serotypes. Using our novel computational approach, we have identified three peptide vaccine candidates that have high potential to induce both B- and T-cell-mediated immune responses from our identified two dual targets. These two targets were modeled and subjected to virtual screening against natural compounds derived from Piper betel. Seven compounds were identified first time from Piper betel to be highly effective to render the function of these targets to identify them as emerging potential drugs against Vibrio. Our preliminary validation suggests that these identified peptide vaccines and betel compounds are highly effective against Vibrio cholerae. Currently we are exhaustively validating these targets, candidate peptide vaccines, and betel derived lead compounds against a number of Vibrio species.
Acesso aberto (Open Access)
Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis
(BioMed Central Ltd, 2014) HASSAN, Syed Shah; TIWARI, Sandeep; GUIMARÃES, Luís Carlos; BACHA, Syed Babar Jamal; FOLADOR, Edson Luiz; SHARMA, Neha Barve; SOARES, Siomar de Castro; ALMEIDA, Sintia Silva de; ALI, Amjad; ISLAM, Arshad; PÓVOA, Fabiana Dias; ABREU, Vinicius Augusto Carvalho de; JAIN, Neha; FERREIRA, Rafaela Salgado; BHATTACHARYA, Antaripa; JUNEJA, Lucky; MIYOSHI, Anderson; SILVA, Artur Luiz da Costa da; BARH, Debmalya; TURJANSKI, Adrian Gustavo; AZEVEDO, Vasco Ariston de Carvalho
Corynebacterium pseudotuberculosis (Cp) is a pathogenic bacterium that causes caseous lymphadenitis (CLA), ulcerative lymphangitis, mastitis, and edematous to a broad spectrum of hosts, including ruminants, thereby threatening economic and dairy industries worldwide. Currently there is no effective drug or vaccine available against Cp. To identify new targets, we adopted a novel integrative strategy, which began with the prediction of the modelome (tridimensional protein structures for the proteome of an organism, generated through comparative modeling) for 15 previously sequenced C. pseudotuberculosis strains. This pan-modelomics approach identified a set of 331 conserved proteins having 95-100% intra-species sequence similarity. Next, we combined subtractive proteomics and modelomics to reveal a set of 10 Cp proteins, which may be essential for the bacteria. Of these, 4 proteins (tcsR, mtrA, nrdI, and ispH) were essential and non-host homologs (considering man, horse, cow and sheep as hosts) and satisfied all criteria of being putative targets. Additionally, we subjected these 4 proteins to virtual screening of a drug-like compound library. In all cases, molecules predicted to form favorable interactions and which showed high complementarity to the target were found among the top ranking compounds. The remaining 6 essential proteins (adk, gapA, glyA, fumC, gnd, and aspA) have homologs in the host proteomes. Their active site cavities were compared to the respective cavities in host proteins. We propose that some of these proteins can be selectively targeted using structure-based drug design approaches (SBDD). Our results facilitate the selection of C. pseudotuberculosis putative proteins for developing broad-spectrum novel drugs and vaccines. A few of the targets identified here have been validated in other microorganisms, suggesting that our modelome strategy is effective and can also be applicable to other pathogens.
Acesso aberto (Open Access)
Quadruplex PCR assay for identification of Corynebacterium pseudotuberculosis differentiating biovar Ovis and Equi
(BioMed Central Ltd, 2017) ALMEIDA, Sintia Silva de; DORNELES, Elaine Maria Seles; DINIZ, Carlos Augusto Almeida; ABREU, Vinicius Augusto Carvalho de; SOUSA, Cassiana Severiano de; ALVES, Jorianne Thyeska Castro; CARNEIRO, Adriana Ribeiro; VILAS BOAS, Priscilla Carolinne Bagano; SPIER, Sharon; BARH, Debmalya; LAGE, Andrey Pereira; FIGUEIREDO, Henrique Cesar Pereira; AZEVEDO, Vasco Ariston de Carvalho
Background: Corynebacterium pseudotuberculosis is classified into two biovars, nitrate-negative biovar Ovis which is the etiologic agent of caseous lymphadenitis in small ruminants and nitrate-positive biovar Equi, which causes abscesses and ulcerative lymphangitis in equines. The aim of this study was to develop a quadruplex PCR assay that would allow simultaneous detection and biovar-typing of C. pseudotuberculosis. Methods: In the present study, genomes of C. pseudotuberculosis strains were used to identify the genes involved in the nitrate reduction pathway to improve a species identification three-primer multiplex PCR assay. The nitrate reductase gene (narG) was included in the PCR assay along with the 16S, rpoB and pld genes to enhance the diagnosis of the multiplex PCR at biovar level. Results: A novel quadruplex PCR assay for C. pseudotuberculosis species and biovar identification was developed. The results of the quadruplex PCR of 348 strains, 346 previously well-characterized clinical isolates of C. pseudotuberculosis from different hosts (goats, sheep, horse, cattle, buffalo, llamas and humans), the vaccine strain 1002 and the type strain ATCC 19410T , were compared to the results of nitrate reductase identification by biochemical test. The McNemar’s Chi-squared test used to compare the two methods used for C. pseudotuberculosis biovar identification showed no significant difference (P = 0.75) [95% CI for odds ratio (0.16–6.14)] between the quadruplex PCR and the nitrate biochemical test. Concordant results were observed for 97.13% (338 / 348) of the tested strains and the kappa value was 0.94 [95% CI (0.90–0.98)]. Conclusions: The ability of the quadruplex assay to discriminate between C. pseudotuberculosis biovar Ovis and Equi strains enhances its usefulness in the clinical microbiology laboratory.
Acesso aberto (Open Access)
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome
(BioMed Central Ltd, 2012) SANTOS, Anderson Rodrigues dos; CARNEIRO, Adriana Ribeiro; GALA-GARCÍA, Alfonso; GOMIDE, Anne Cybelle Pinto; BARH, Debmalya; BARBOSA, Eudes Guilherme Vieira; ABURJAILE, Flavia Figueira; DORELLA, Fernanda Alves; ROCHA, Flávia de Souza; GUIMARÃES, Luís Carlos; TURK, Meritxell Zurita; RAMOS, Rommel Thiago Juca; ALMEIDA, Sintia Silva de; SOARES, Siomar de Castro; PEREIRA, Ulisses de Pádua; ABREU, Vinicius Augusto Carvalho de; SILVA, Artur Luiz da Costa da; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho
Background: Pan-genomic studies aim, for instance, at defining the core, dispensable and unique genes within a species. A pan-genomics study for vaccine design tries to assess the best candidates for a vaccine against a specific pathogen. In this context, rather than studying genes predicted to be exported in a single genome, with pan genomics it is possible to study genes present in different strains within the same species, such as virulence factors. The target organism of this pan-genomic work here presented is Corynebacterium pseudotuberculosis, the etiologic agent of caseous lymphadenitis (CLA) in goat and sheep, which causes significant economic losses in those herds around the world. Currently, only a few antigens against CLA are known as being the basis of commercial and still ineffective vaccines. In this regard, the here presented work analyses, in silico, five C. pseudotuberculosis genomes and gathers data to predict common exported proteins in all five genomes. These candidates were also compared to two recent C. pseudotuberculosis in vitro exoproteome results. Results: The complete genome of five C. pseudotuberculosis strains (1002, C231, I19, FRC41 and PAT10) were submitted to pan-genomics analysis, yielding 306, 59 and 12 gene sets, respectively, representing the core, dispensable and unique in silico predicted exported pan-genomes. These sets bear 150 genes classified as secreted (SEC) and 227 as potentially surface exposed (PSE). Our findings suggest that the main C. pseudotuberculosis in vitro exoproteome could be greater, appended by a fraction of the 35 proteins formerly predicted as making part of the variant in vitro exoproteome. These genomes were manually curated for correct methionine initiation and redeposited with a total of 1885 homogenized genes. Conclusions: The in silico prediction of exported proteins has allowed to define a list of putative vaccine candidate genes present in all five complete C. pseudotuberculosis genomes. Moreover, it has also been possible to define the in silico predicted dispensable and unique C. pseudotuberculosis exported proteins. These results provide in silico evidence to further guide experiments in the areas of vaccines, diagnosis and drugs. The work here presented is the first whole C. pseudotuberculosis in silico predicted pan-exoproteome completed till today.
Acesso aberto (Open Access)
Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina
(American Society for Microbiology, 2011-11) CERDEIRA, Louise Teixeira; GOMIDE, Anne Cybelle Pinto; SCHNEIDER, Maria Paula Cruz; ALMEIDA, Sintia Silva de; SANTOS, Anderson Rodrigues dos; BARBOSA, Eudes Guilherme Vieira; ALI, Amjad; BARBOSA, Maria Silvanira Ribeiro; CARNEIRO, Adriana Ribeiro; RAMOS, Rommel Thiago Juca; OLIVEIRA, Rodrigo Santos de; BARH, Debmalya; SHARMA, Neha Barve; ZAMBARE, Vasudeo; BELCHIOR, Silvia Estevão; GUIMARÃES, Luís Carlos; SOARES, Siomar de Castro; DORELLA, Fernanda Alves; ROCHA, Flávia de Souza; ABREU, Vinicius Augusto Carvalho de; TAUCH, Andreas; TROST, Eva; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho; SILVA, Artur Luiz da Costa da
In this work, we report the complete genome sequence of a Corynebacterium pseudotuberculosis PAT10 isolate, collected from a lung abscess in an Argentine sheep in Patagonia, whose pathogen also required an investigation of its pathogenesis. Thus, the analysis of the genome sequence offers a means to better understanding of the molecular and genetic basis of virulence of this bacterium.
Acesso aberto (Open Access)
Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp162, Isolated from Camel
(American Society for Microbiology, 2012) HASSAN, Syed Shah; SCHNEIDER, Maria Paula Cruz; RAMOS, Rommel Thiago Juca; CARNEIRO, Adriana Ribeiro; LIMA, Alex Ranieri Jerônimo; GUIMARÃES, Luís Carlos; ALI, Amjad; BAKHTIAR, Syeda Marriam; PEREIRA, Ulisses de Pádua; SANTOS, Anderson Rodrigues dos; SOARES, Siomar de Castro; DORELLA, Fernanda Alves; GOMIDE, Anne Cybelle Pinto; RIBEIRO, Dayana; BARBOSA, Maria Silvanira Ribeiro; ALMEIDA, Sintia Silva de; ABREU, Vinicius Augusto Carvalho de; ABURJAILE, Flavia Figueira; NASCIMENTO, Karina Kelly Fiaux do; BARBOSA, Eudes Guilherme Vieira; DINIZ, Carlos Augusto Almeida; ROCHA, Flávia de Souza; SAXENA, Rashmi; TIWARI, Sandeep; ZAMBARE, Vasudeo; GHOSH, Preetam; PACHECO, Luis Gustavo Carvalho; DOWSON, Christopher G.; KUMAR, Anil; BARH, Debmalya; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho; SILVA, Artur Luiz da Costa da
Corynebacterium pseudotuberculosis is a pathogen of great veterinary and economic importance, since it affects livestock, mainly sheep and goats, worldwide, together with reports of its presence in camels in several Arabic, Asiatic, and East and West African countries, as well as Australia. In this article, we report the genome sequence of Corynebacterium pseudotuberculosis strain Cp162, collected from the external neck abscess of a camel in the United Kingdom.