1
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Jesus HNR, Ramos JN, Rocha DJPG, Alves DA, Silva CS, Cruz JVO, Vieira VV, Souza C, Santos LS, Navas J, Ramos RTJ, Azevedo V, Aguiar ERGR, Mattos-Guaraldi AL, Pacheco LGC. The pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum. Funct Integr Genomics 2022; 23:5. [PMID: 36534203 DOI: 10.1007/s10142-022-00932-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
Abstract
Corynebacterium striatum, a common constituent of the human skin microbiome, is now considered an emerging multidrug-resistant pathogen of immunocompromised and chronically ill patients. However, little is known about the molecular mechanisms in the transition from colonization to the multidrug-resistant (MDR) invasive phenotype in clinical isolates. This study performed a comprehensive pan-genomic analysis of C. striatum, including isolates from "normal skin microbiome" and from MDR infections, to gain insights into genetic factors contributing to pathogenicity and multidrug resistance in this species. For this, three novel genome sequences were obtained from clinical isolates of C. striatum of patients from Brazil, and other 24 complete or draft C. striatum genomes were retrieved from GenBank, including the ATCC6940 isolate from the Human Microbiome Project. Analysis of C. striatum strains demonstrated the presence of an open pan-genome (α = 0.852803) containing 3816 gene families, including 15 antimicrobial resistance (AMR) genes and 32 putative virulence factors. The core and accessory genomes included 1297 and 1307 genes, respectively. The identified AMR genes are primarily associated with resistance to aminoglycosides and tetracyclines. Of these, 66.6% are present in genomic islands, and four AMR genes, including aac(6')-ib7, are located in a class 1-integron. In conclusion, our data indicated that C. striatum possesses genomic characteristics favorable to the invasive phenotype, with high genomic plasticity, a robust genetic arsenal for iron acquisition, and important virulence determinants and AMR genes present in mobile genetic elements.
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Affiliation(s)
- Hendor N R Jesus
- Multicenter Post-Graduate Program in Biochemistry and Molecular Biology (PMBqBM), Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Juliana N Ramos
- Laboratory of Diphtheria and Corinebacteria of Clinical Relevance, School of Medical Sciences, Rio de Janeiro State University - LDCIC/FCM/UERJ, Rio de Janeiro, RJ, Brazil
| | - Danilo J P G Rocha
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Daniele A Alves
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil.,Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carolina S Silva
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - João V O Cruz
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Verônica V Vieira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório Interdisciplinar de Pesquisas Médicas, Rio de Janeiro, RJ, Brazil
| | - Cassius Souza
- Laboratory of Diphtheria and Corinebacteria of Clinical Relevance, School of Medical Sciences, Rio de Janeiro State University - LDCIC/FCM/UERJ, Rio de Janeiro, RJ, Brazil
| | - Louisy S Santos
- Laboratory of Diphtheria and Corinebacteria of Clinical Relevance, School of Medical Sciences, Rio de Janeiro State University - LDCIC/FCM/UERJ, Rio de Janeiro, RJ, Brazil
| | - Jesus Navas
- Cantabria University, Instituto de Investigación Valdecilla (IDIVAL), Santander, Spain
| | - Rommel T J Ramos
- Institute of Biological Sciences, Federal University of Para, Belem, PA, Brazil.,Biological Engineering Laboratory, Science and Technology Park Guama, Belem, PA, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eric R G R Aguiar
- Department of Biological Sciences, State University of Santa Cruz, Ilhéus, BA, Brazil
| | - Ana L Mattos-Guaraldi
- Laboratory of Diphtheria and Corinebacteria of Clinical Relevance, School of Medical Sciences, Rio de Janeiro State University - LDCIC/FCM/UERJ, Rio de Janeiro, RJ, Brazil
| | - Luis G C Pacheco
- Multicenter Post-Graduate Program in Biochemistry and Molecular Biology (PMBqBM), Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil. .,Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil.
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2
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Felice AG, Santos LNQ, Kolossowski I, Zen FL, Alves LG, Rodrigues TCV, Prado LCS, Jaiswal AK, Tiwari S, Miranda FM, Ramos RTJ, Azevedo V, Oliveira CJF, Benevides LJ, Soares SC. Comparative genomics of Bordetella pertussis and prediction of new vaccines and drug targets. J Biomol Struct Dyn 2022; 40:10136-10152. [PMID: 34155952 DOI: 10.1080/07391102.2021.1940279] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pertussis is a highly contagious respiratory disease caused by Bordetella pertussis, a Gram-negative bacterium described over a century ago. Despite broad vaccine coverage and treatment options, the disease is remerging as a public health problem especially in infants and older children. Recent data indicate re-emergence of the disease is related to bacterial resistance to immune defences and decreased vaccine effectiveness, which obviously suggests the need of new effective vaccines and drugs. In an attempt to contribute with solutions to this great challenge, bioinformatics tools were used to genetically comprehend the species of these bacteria and predict new vaccines and drug targets. In fact, approaches were used to analysis genomic plasticity, gene synteny and species similarities between the 20 genomes of Bordetella pertussis already available. Furthermore, it was conducted reverse vaccinology and docking analysis to identify proteins with potential to become vaccine and drug targets, respectively. The analyses showed the 20 genomes belongs to a homogeneous group that has preserved most of the genes over time. Besides that, were found genomics islands and good proteins to be candidates for vaccine and drugs. Taken together, these results suggests new possibilities that may be useful to develop new vaccines and drugs that will help the prevention and treatment strategies of pertussis disease caused by these Bordetella strains. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Andrei G Felice
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Leonardo N Q Santos
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Ian Kolossowski
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Felipe L Zen
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Leandro G Alves
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Thaís C V Rodrigues
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ligia C S Prado
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Arun K Jaiswal
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fábio M Miranda
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.,Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Minas Gerais, Brazil
| | - Rommel T J Ramos
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.,Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Carlo J F Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Leandro J Benevides
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Siomar C Soares
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
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3
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Jesus HNR, Rocha DJPG, Ramos RTJ, Silva A, Brenig B, Góes-Neto A, Costa MM, Soares SC, Azevedo V, Aguiar ERGR, Martínez-Martínez L, Ocampo A, Alibi S, Dorta A, Pacheco LGC, Navas J. Pan-genomic analysis of Corynebacterium amycolatum gives insights into molecular mechanisms underpinning the transition to a pathogenic phenotype. Front Microbiol 2022; 13:1011578. [DOI: 10.3389/fmicb.2022.1011578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022] Open
Abstract
Corynebacterium amycolatum is a nonlipophilic coryneform which is increasingly being recognized as a relevant human and animal pathogen showing multidrug resistance to commonly used antibiotics. However, little is known about the molecular mechanisms involved in transition from colonization to the MDR invasive phenotype in clinical isolates. In this study, we performed a comprehensive pan-genomic analysis of C. amycolatum, including 26 isolates from different countries. We obtained the novel genome sequences of 8 of them, which are multidrug resistant clinical isolates from Spain and Tunisia. They were analyzed together with other 18 complete or draft C. amycolatum genomes retrieved from GenBank. The species C. amycolatum presented an open pan-genome (α = 0.854905), with 3,280 gene families, being 1,690 (51.52%) in the core genome, 1,121 related to accessory genes (34.17%), and 469 related to unique genes (14.29%). Although some classic corynebacterial virulence factors are absent in the species C. amycolatum, we did identify genes associated with immune evasion, toxin, and antiphagocytosis among the predicted putative virulence factors. Additionally, we found genomic evidence for extensive acquisition of antimicrobial resistance genes through genomic islands.
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Fortunato Costa K, Almeida Araújo F, Morais J, Lisboa Frances CR, Ramos RTJ. Text mining for identification of biological entities related to antibiotic resistant organisms. PeerJ 2022; 10:e13351. [PMID: 35539017 PMCID: PMC9080439 DOI: 10.7717/peerj.13351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 04/07/2022] [Indexed: 01/13/2023] Open
Abstract
Antimicrobial resistance is a significant public health problem worldwide. In recent years, the scientific community has been intensifying efforts to combat this problem; many experiments have been developed, and many articles are published in this area. However, the growing volume of biological literature increases the difficulty of the biocuration process due to the cost and time required. Modern text mining tools with the adoption of artificial intelligence technology are helpful to assist in the evolution of research. In this article, we propose a text mining model capable of identifying and ranking prioritizing scientific articles in the context of antimicrobial resistance. We retrieved scientific articles from the PubMed database, adopted machine learning techniques to generate the vector representation of the retrieved scientific articles, and identified their similarity with the context. As a result of this process, we obtained a dataset labeled "Relevant" and "Irrelevant" and used this dataset to implement one supervised learning algorithm to classify new records. The model's overall performance reached 90% accuracy and the f-measure (harmonic mean between the metrics) reached 82% accuracy for positive class and 93% for negative class, showing quality in the identification of scientific articles relevant to the context. The dataset, scripts and models are available at https://github.com/engbiopct/TextMiningAMR.
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Affiliation(s)
- Kelle Fortunato Costa
- Programa de pós-graduação em Engenharia Elétrica, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Fabrício Almeida Araújo
- Biological Science Institute, Universidade Federal do Pará, Belém, Pará, Brazil,Universidade Federal Rural da Amazônia, Belém, Pará, Brazil
| | | | | | - Rommel T. J. Ramos
- Biological Science Institute, Universidade Federal do Para, Belém, Pará, Brazil
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5
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Nogueira WG, Jaiswal AK, Tiwari S, Ramos RTJ, Ghosh P, Barh D, Azevedo V, Soares SC. Computational identification of putative common genomic drug and vaccine targets in Mycoplasma genitalium. Genomics 2021; 113:2730-2743. [PMID: 34118385 DOI: 10.1016/j.ygeno.2021.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/17/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
Mycoplasma genitalium is an obligate intracellular bacterium that is responsible for several sexually transmitted infections, including non-gonococcal urethritis in men and several inflammatory reproductive tract syndromes in women. Here, we applied subtractive genomics and reverse vaccinology approaches for in silico prediction of potential vaccine and drug targets against five strains of M. genitalium. We identified 403 genes shared by all five strains, from which 104 non-host homologous proteins were selected, comprising of 44 exposed/secreted/membrane proteins and 60 cytoplasmic proteins. Based on the essentiality, functionality, and structure-based binding affinity, we finally predicted 19 (14 novel) putative vaccine and 7 (2 novel) candidate drug targets. The docking analysis showed six molecules from the ZINC database as promising drug candidates against the identified targets. Altogether, both vaccine candidates and drug targets identified here may contribute to the future development of therapeutic strategies to control the spread of M. genitalium worldwide.
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Affiliation(s)
- Wylerson G Nogueira
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Arun Kumar Jaiswal
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.; Department of Immunology, Microbiology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil..
| | - Rommel T J Ramos
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond VA-23284, USA
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Siomar C Soares
- Department of Immunology, Microbiology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil.
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6
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Felice AG, Alves LG, Freitas ASF, Rodrigues TCV, Jaiswal AK, Tiwari S, Gomes LGR, Miranda FM, Ramos RTJ, Azevedo V, Oliveira LC, Oliveira CJ, Soares SDC, Benevides LJ. Pan-genomic analyses of 47 complete genomes of the Rickettsia genus and prediction of new vaccine targets and virulence factors of the species. J Biomol Struct Dyn 2021; 40:7496-7510. [PMID: 33719856 DOI: 10.1080/07391102.2021.1898473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The genus Rickettsia belongs to the Proteobacteria phylum and these bacteria infect animals and humans causing a range of diseases worldwide. The genus is divided into 4 groups and despite the public health threat and the knowledge accumulated so far, the mandatory intracellular bacteria behaviour and limitation for in vitro culture makes it difficult to create new vaccines and drug targets to these bacteria. In an attempt to overcome these limitations, pan-genomic approaches has used 47 genomes of the genus Rickettsia, in order to describe species similarities and genomics islands. Moreover, we conducted reverse vaccinology and docking analysis aiming the identification of proteins that have great potential to become vaccine and drug targets. We found out that the bacteria of the four Rickettsia groups have a high similarity with each other, with about 90 to 100% of identity. A pathogenicity island and a resistance island were predicted. In addition, 8 proteins were also predicted as strong candidates for vaccine and 9 as candidates for drug targets. The prediction of the proteins leads us to believe in a possibility of prospecting potential drugs or creating a polyvalent vaccine, which could reach most strains of this large group of bacteria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Andrei G Felice
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triangulo Mineiro, Uberaba, MG, Brazil
| | - Leandro G Alves
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triangulo Mineiro, Uberaba, MG, Brazil
| | - Alissa S F Freitas
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triangulo Mineiro, Uberaba, MG, Brazil
| | - Thaís C V Rodrigues
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Arun K Jaiswal
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lucas G R Gomes
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fábio M Miranda
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rommel T J Ramos
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.,Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Minas Gerais, Brazil
| | - Letícia C Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triangulo Mineiro, Uberaba, MG, Brazil
| | - Carlo J Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triangulo Mineiro, Uberaba, MG, Brazil
| | - Siomar D C Soares
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triangulo Mineiro, Uberaba, MG, Brazil
| | - Leandro J Benevides
- Bioinformatics Laboratory, National Laboratory for Scientific Computing, Petrópolis, Rio de Janeiro, Brazil
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7
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Freitas DY, Araújo S, Folador ARC, Ramos RTJ, Azevedo JSN, Tacão M, Silva A, Henriques I, Baraúna RA. Extended Spectrum Beta-Lactamase-Producing Gram-Negative Bacteria Recovered From an Amazonian Lake Near the City of Belém, Brazil. Front Microbiol 2019; 10:364. [PMID: 30873145 PMCID: PMC6403167 DOI: 10.3389/fmicb.2019.00364] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/12/2019] [Indexed: 12/14/2022] Open
Abstract
Aquatic systems have been described as antibiotic resistance reservoirs, where water may act as a vehicle for the spread of resistant bacteria and resistance genes. We evaluated the occurrence and diversity of third generation cephalosporin-resistant gram-negative bacteria in a lake in the Amazonia region. This water is used for human activities, including consumption after appropriate treatment. Eighteen samples were obtained from six sites in October 2014. Water quality parameters were generally within the legislation limits. Thirty-three bacterial isolates were identified as Escherichia (n = 7 isolates), Acinetobacter, Enterobacter, and Klebsiella (n = 5 each), Pseudomonas (n = 4), Shigella (n = 3), and Chromobacterium, Citrobacter, Leclercia, Phytobacter (1 isolate each). Twenty nine out of 33 isolates (88%) were resistant to most beta-lactams, except carbapenems, and 88% (n = 29) were resistant to antibiotics included in at least three different classes. Among the beta-lactamase genes inspected, the blaCTX–M was the most prevalent (n = 12 positive isolates), followed by blaTEM (n = 5) and blaSHV (n = 4). blaCTX–M–15 (n = 5), blaCTX–M–14 (n = 1) and blaCTX–M–2 (n = 1) variants were detected in conserved genomic contexts: blaCTX–M–15 flanked by ISEcp1 and Orf477; blaCTX–M–14 flanked by ISEcp1 and IS903; and blaCTX–M–2 associated to an ISCR element. For 4 strains the transfer of blaCTX–M was confirmed by conjugation assays. Compared with the recipient, the transconjugants showed more than 500-fold increases in the MICs of cefotaxime and 16 to 32-fold increases in the MICs of ceftazidime. Two isolates (Escherichia coli APC43A and Acinetobacter baumannii APC25) were selected for whole genome analysis. APC43A was predicted as a E. coli pathogen of the high-risk clone ST471 and serotype O154:H18. blaCTX–M–15 as well as determinants related to efflux of antibiotics, were noted in APC43A genome. A. baumannii APC25 was susceptible to carbapenems and antibiotic resistance genes detected in its genome were intrinsic determinants (e.g., blaOXA–208 and blaADC–like). The strain was not predicted as a human pathogen and belongs to a new sequence type. Operons related to metal resistance were predicted in both genomes as well as pathogenicity and resistance islands. Results suggest a high dissemination of ESBL-producing bacteria in Lake Água Preta which, although not presenting characteristics of a strongly impacted environment, contains multi-drug resistant pathogenic strains.
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Affiliation(s)
- Dhara Y Freitas
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Susana Araújo
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Adriana R C Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Rommel T J Ramos
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | - Marta Tacão
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Isabel Henriques
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Rafael A Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
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8
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de Sousa AL, Maués D, Lobato A, Franco EF, Pinheiro K, Araújo F, Pantoja Y, da Costa da Silva AL, Morais J, Ramos RTJ. PhageWeb - Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes. Front Genet 2018; 9:644. [PMID: 30619469 PMCID: PMC6305541 DOI: 10.3389/fgene.2018.00644] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/27/2018] [Indexed: 12/04/2022] Open
Abstract
This study developed a computational tool with a graphical interface and a web-service that allows the identification of phage regions through homology search and gene clustering. It uses G+C content variation evaluation and tRNA prediction sites as evidence to reinforce the presence of prophages in indeterminate regions. Also, it performs the functional characterization of the prophages regions through data integration of biological databases. The performance of PhageWeb was compared to other available tools (PHASTER, Prophinder, and PhiSpy) using Sensitivity (Sn) and Positive Predictive Value (PPV) tests. As a reference for the tests, more than 80 manually annotated genomes were used. In the PhageWeb analysis, the Sn index was 86.1% and the PPV was approximately 87%, while the second best tool presented Sn and PPV values of 83.3 and 86.5%, respectively. These numbers allowed us to observe a greater precision in the regions identified by PhageWeb while compared to other prediction tools submitted to the same tests. Additionally, PhageWeb was much faster than the other computational alternatives, decreasing the processing time to approximately one-ninth of the time required by the second best software. PhageWeb is freely available at http://computationalbiology.ufpa.br/phageweb.
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Affiliation(s)
| | - Dener Maués
- Institute of Exact and Natural Sciences, Federal University of Para, Belém, Brazil
| | - Amália Lobato
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
| | - Edian F. Franco
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
| | - Kenny Pinheiro
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
| | - Fabrício Araújo
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
| | - Yan Pantoja
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
| | | | - Jefferson Morais
- Institute of Exact and Natural Sciences, Federal University of Para, Belém, Brazil
| | - Rommel T. J. Ramos
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
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9
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Dias LM, Folador ARC, Oliveira AM, Ramos RTJ, Silva A, Baraúna RA. Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome. Genome Biol Evol 2018; 10:731-741. [PMID: 29438502 PMCID: PMC5833320 DOI: 10.1093/gbe/evy029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2018] [Indexed: 11/12/2022] Open
Abstract
Exiguobacterium and Psychrobacter are bacterial genera with several cold-adapted species. These extremophiles are commonly isolated from the same habitats in Earth's cryosphere and have great ecological and biotechnological relevance. Thus, through comparative genomic analyses, it was possible to understand the functional diversity of these psychrotrophic and psychrophilic species and present new insights into the microbial adaptation to cold. The nucleotide identity between Exiguobacterium genomes was >90%. Three genomic islands were identified in the E. antarcticum B7 genome. These islands contained genes involved in flagella biosynthesis and chemotaxis, as well as enzymes for carotenoid biosynthesis. Clustering of cold shock proteins by Ka/Ks ratio suggests the occurrence of a positive selection over these genes. Neighbor-joining clustering of complete genomes showed that the E. sibiricum was the most closely related to E. antarcticum. A total of 92 genes were shared between Exiguobacterium and Psychrobacter. A reduction in the genomic content of E. antarcticum B7 was observed. It presented the smallest genome size of its genus and a lower number of genes because of the loss of many gene families compared with the other genomes. In our study, eight genomes of Exiguobacterium and Psychrobacter were compared and analysed. Psychrobacter showed higher genomic plasticity and E. antarcticum B7 presented a large decrease in genomic content without changing its ability to grow in cold environments.
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Affiliation(s)
- Larissa M Dias
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Adriana R C Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Amanda M Oliveira
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Rommel T J Ramos
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Rafael A Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
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Buscardo E, Geml J, Schmidt SK, Silva ALC, Ramos RTJ, Barbosa SMR, Andrade SS, Dalla Costa R, Souza AP, Freitas H, Cunha HB, Nagy L. Of mammals and bacteria in a rainforest: Temporal dynamics of soil bacteria in response to simulated N pulse from mammalian urine. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12998] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erika Buscardo
- Centre for Functional EcologyUniversity of Coimbra Coimbra Portugal
- Department of Plant BiologyUniversity of Campinas Campinas Brazil
- Large‐scale Biosphere‐Atmosphere ProgrammeNational Amazonian Research Institute (INPA) Manaus Brazil
| | - József Geml
- Biodiversity Dynamics Research GroupNaturalis Biodiversity Center Leiden The Netherlands
- Faculty of SciencesLeiden University Leiden The Netherlands
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary BiologyUniversity of Colorado Boulder CO USA
| | | | | | | | | | | | - Anete P. Souza
- Department of Plant BiologyUniversity of Campinas Campinas Brazil
| | - Helena Freitas
- Centre for Functional EcologyUniversity of Coimbra Coimbra Portugal
| | - Hillândia B. Cunha
- Large‐scale Biosphere‐Atmosphere ProgrammeNational Amazonian Research Institute (INPA) Manaus Brazil
| | - Laszlo Nagy
- Department of Plant BiologyUniversity of Campinas Campinas Brazil
- Large‐scale Biosphere‐Atmosphere ProgrammeNational Amazonian Research Institute (INPA) Manaus Brazil
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11
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Baraúna RA, Ramos RTJ, Veras AAO, Pinheiro KC, Benevides LJ, Viana MVC, Guimarães LC, Edman JM, Spier SJ, Azevedo V, Silva A. Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics. PLoS One 2017; 12:e0170676. [PMID: 28125655 PMCID: PMC5268413 DOI: 10.1371/journal.pone.0170676] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/09/2017] [Indexed: 12/21/2022] Open
Abstract
Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp. This bacterium is the causative agent of disease known as "pigeon fever" which commonly affects horses worldwide. The pangenome of biovar equi was calculated and two phylogenomic approaches were used to identify clustering patterns within Corynebacterium genus. Furthermore, other comparative analyses were performed including the prediction of genomic islands and prophages, and SNP-based phylogeny. In the phylogenomic tree, C. pseudotuberculosis was divided into two distinct clades, one formed by nitrate non-reducing species (biovar ovis) and another formed by nitrate-reducing species (biovar equi). In the latter group, the strains isolated from California were more related to each other, while the strains CIP 52.97 and 1/06-A formed the outermost clade of the biovar equi. A total of 1,355 core genes were identified, corresponding to 42.5% of the pangenome. This pangenome has one of the smallest core genomes described in the literature, suggesting a high genetic variability of biovar equi of C. pseudotuberculosis. The analysis of the similarity between the resistance islands identified a higher proximity between the strains that caused more severe infectious conditions (infection in the internal organs). Pathogenicity islands were largely conserved between strains. Several genes that modulate the pathogenicity of C. pseudotuberculosis were described including peptidases, recombination enzymes, micoside synthesis enzymes, bacteriocins with antimicrobial activity and several others. Finally, no genotypic differences were observed between the strains that caused the three different types of infection (external abscess formation, infection with abscess formation in the internal organs, and ulcerative lymphangitis). Instead, it was noted that there is a higher phenetic correlation between strains isolated at California compared to the other strains. Additionally, high variability of resistance islands suggests gene acquisition through several events of horizontal gene transfer.
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Affiliation(s)
- Rafael A. Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel T. J. Ramos
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Adonney A. O. Veras
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Kenny C. Pinheiro
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Leandro J. Benevides
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcus V. C. Viana
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luís C. Guimarães
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Judy M. Edman
- School of Veterinary Medicine, Department of Medicine and Epidemiology, University of California Davis, Davis, California, United States of America
| | - Sharon J. Spier
- School of Veterinary Medicine, Department of Medicine and Epidemiology, University of California Davis, Davis, California, United States of America
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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12
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Mariano DCB, Pereira FL, Aguiar EL, Oliveira LC, Benevides L, Guimarães LC, Folador EL, Sousa TJ, Ghosh P, Barh D, Figueiredo HCP, Silva A, Ramos RTJ, Azevedo VAC. SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology. BMC Bioinformatics 2016; 17:456. [PMID: 28105921 PMCID: PMC5249034 DOI: 10.1186/s12859-016-1344-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. RESULTS In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. CONCLUSION Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .
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Affiliation(s)
- Diego C. B. Mariano
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Felipe L. Pereira
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Edgar L. Aguiar
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Letícia C. Oliveira
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Leandro Benevides
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Luís C. Guimarães
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Edson L. Folador
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Thiago J. Sousa
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Preetam Ghosh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, PurbaMedinipur WB-721172 India
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA USA
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, PurbaMedinipur WB-721172 India
| | - Henrique C. P. Figueiredo
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará Brazil
| | - Rommel T. J. Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará Brazil
| | - Vasco A. C. Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
- Federal University of Minas Gerais, Institute of Biological Sciences, Antônio Carlos 6627, Pampulha, 30161-970 Belo Horizonte, Minas Gerais Brazil
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13
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de Sá PHCG, Miranda F, Veras A, de Melo DM, Soares S, Pinheiro K, Guimarães L, Azevedo V, Silva A, Ramos RTJ. GapBlaster-A Graphical Gap Filler for Prokaryote Genomes. PLoS One 2016; 11:e0155327. [PMID: 27171416 PMCID: PMC4865197 DOI: 10.1371/journal.pone.0155327] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/27/2016] [Indexed: 11/17/2022] Open
Abstract
The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer.
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Affiliation(s)
- Pablo H C G de Sá
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Fábio Miranda
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Adonney Veras
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | | | - Siomar Soares
- Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Kenny Pinheiro
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Luis Guimarães
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel T J Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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14
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de Sá PHCG, Veras AAO, Carneiro AR, Barúna RA, Guimarães LC, Pinheiro KC, Pinto AC, Soares SC, Schneider MPC, Azevedo V, Silva A, Ramos RTJ. Corynebacterium pseudotuberculosis RNA-seq data from abiotic stresses. Data Brief 2015; 5:963-6. [PMID: 26702428 PMCID: PMC4669661 DOI: 10.1016/j.dib.2015.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/22/2015] [Accepted: 11/06/2015] [Indexed: 10/28/2022] Open
Abstract
Corynebacterium pseudotuberculosis causes significant loss to goat and sheep farmers because it is the causal agent of the infectious disease caseous lymphadenitis, which may lead to outcomes ranging from skin injury to animal death (Ruiz et al., 2011) [1]. This bacterium was grown under osmotic (2 M), acid (pH) and heat (50 °C) stress and under control (Normal-BHI brain heart infusion) conditions, which simulate the conditions faced by the bacteria during the infectious process. Subsequently, cDNA of each condition was sequenced by the SOLiD3 Plus platform using the RNA-Seq technique [2], [3], [4]. The data produced was processed to evaluate the differential gene expression, which is helpful to understand the adaptation mechanisms during the infection in the host. The sequencing data of all conditions are available in the European Bioinformatics Institute (EBI) repository under accession number E-MTAB-2017.
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Affiliation(s)
- Pablo H C G de Sá
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Adonney A O Veras
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Adriana R Carneiro
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rafael A Barúna
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Luís C Guimarães
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Kenny C Pinheiro
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Anne C Pinto
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Siomar C Soares
- Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Maria P C Schneider
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel T J Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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15
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Pacheco LGC, Mattos-Guaraldi AL, Santos CS, Veras AAO, Guimarães LC, Abreu V, Pereira FL, Soares SC, Dorella FA, Carvalho AF, Leal CG, Figueiredo HCP, Ramos JN, Vieira VV, Farfour E, Guiso N, Hirata R, Azevedo V, Silva A, Ramos RTJ. Draft Genome Sequences of Two Species of "Difficult-to-Identify" Human-Pathogenic Corynebacteria: Implications for Better Identification Tests. J Genomics 2015; 3:82-4. [PMID: 26516374 PMCID: PMC4618292 DOI: 10.7150/jgen.12886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
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 encoding 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.
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Affiliation(s)
- Luis G C Pacheco
- 1. Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Ana L Mattos-Guaraldi
- 2. Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Carolina S Santos
- 1. Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Adonney A O Veras
- 3. Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Luis C Guimarães
- 3. Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil. ; 4. Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Vinícius Abreu
- 4. Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Felipe L Pereira
- 5. National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Siomar C Soares
- 5. National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Fernanda A Dorella
- 5. National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Alex F Carvalho
- 5. National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Carlos G Leal
- 5. National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Henrique C P Figueiredo
- 5. National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Juliana N Ramos
- 2. Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil. ; 6. National Institute for Quality Control in Health - Oswaldo Cruz Foundation (INCQS - Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Veronica V Vieira
- 6. National Institute for Quality Control in Health - Oswaldo Cruz Foundation (INCQS - Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Eric Farfour
- 7. Unité de Prévention et Thérapie Moléculaires des Maladies Humaines, Institut Pasteur, Paris, France
| | - Nicole Guiso
- 7. Unité de Prévention et Thérapie Moléculaires des Maladies Humaines, Institut Pasteur, Paris, France
| | - Raphael Hirata
- 2. Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Vasco Azevedo
- 4. Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Artur Silva
- 3. Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Rommel T J Ramos
- 3. Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
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16
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Dall'Agnol HPMB, Baraúna RA, de Sá PHCG, Ramos RTJ, Nóbrega F, Nunes CIP, das Graças DA, Carneiro AR, Santos DM, Pimenta AMC, Carepo MSP, Azevedo V, Pellizari VH, Schneider MPC, Silva A. Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation. BMC Genomics 2014; 15:986. [PMID: 25407400 PMCID: PMC4247613 DOI: 10.1186/1471-2164-15-986] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 10/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Exiguobacterium antarcticum strain B7 is a Gram-positive psychrotrophic bacterial species isolated in Antarctica. Although this bacteria has been poorly studied, its genome has already been sequenced. Therefore, it is an appropriate model for the study of thermal adaptation. In the present study, we analyzed the transcriptomes and proteomes of E. antarcticum B7 grown at 0°C and 37°C by SOLiD RNA-Seq, Ion Torrent RNA-Seq and two-dimensional difference gel electrophoresis tandem mass spectrometry (2D-DIGE-MS/MS). RESULTS We found expression of 2,058 transcripts in all replicates from both platforms and differential expression of 564 genes (absolute log2FC≥1, P-value<0.001) comparing the two temperatures by RNA-Seq. A total of 73 spots were differentially expressed between the two temperatures on 2D-DIGE, 25 of which were identified by MS/MS. Some proteins exhibited patterns of dispersion in the gel that are characteristic of post-translational modifications. CONCLUSIONS Our findings suggest that the two sequencing platforms yielded similar results and that different omic approaches may be used to improve the understanding of gene expression. To adapt to low temperatures, E. antarcticum B7 expresses four of the six cold-shock proteins present in its genome. The cold-shock proteins were the most abundant in the bacterial proteome at 0°C. Some of the differentially expressed genes are required to preserve transcription and translation, while others encode proteins that contribute to the maintenance of the intracellular environment and appropriate protein folding. The results denote the complexity intrinsic to the adaptation of psychrotrophic organisms to cold environments and are based on two omic approaches. They also unveil the lifestyle of a bacterial species isolated in Antarctica.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Artur Silva
- Laboratório de Polimorfismo de DNA, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brasil.
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Carvalho DM, de Sá PH, Castro TLP, Carvalho RD, Pinto A, Gil DJP, Bagano P, Bastos B, Costa LFM, Meyer R, Silva A, Azevedo V, Ramos RTJ, Pacheco LGC. Reference genes for RT-qPCR studies in Corynebacterium pseudotuberculosis identified through analysis of RNA-seq data. Antonie van Leeuwenhoek 2014; 106:605-14. [DOI: 10.1007/s10482-014-0231-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/02/2014] [Indexed: 11/27/2022]
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18
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Pinto AC, de Sá PHCG, Ramos RTJ, Barbosa S, Barbosa HPM, Ribeiro AC, Silva WM, Rocha FS, Santana MP, de Paula Castro TL, Miyoshi A, Schneider MPC, Silva A, Azevedo V. Differential transcriptional profile of Corynebacterium pseudotuberculosis in response to abiotic stresses. BMC Genomics 2014; 15:14. [PMID: 24405787 PMCID: PMC3890534 DOI: 10.1186/1471-2164-15-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 12/13/2013] [Indexed: 11/12/2022] Open
Abstract
Background The completion of whole-genome sequencing for Corynebacterium pseudotuberculosis strain 1002 has contributed to major advances in research aimed at understanding the biology of this microorganism. This bacterium causes significant loss to goat and sheep farmers because it is the causal agent of the infectious disease caseous lymphadenitis, which may lead to outcomes ranging from skin injury to animal death. In the current study, we simulated the conditions experienced by the bacteria during host infection. By sequencing transcripts using the SOLiDTM 3 Plus platform, we identified new targets expected to potentiate the survival and replication of the pathogen in adverse environments. These results may also identify possible candidates useful for the development of vaccines, diagnostic kits or therapies aimed at the reduction of losses in agribusiness. Results Under the 3 simulated conditions (acid, osmotic and thermal shock stresses), 474 differentially expressed genes exhibiting at least a 2-fold change in expression levels were identified. Important genes to the infection process were induced, such as those involved in virulence, defence against oxidative stress, adhesion and regulation, and many genes encoded hypothetical proteins, indicating that further investigation of the bacterium is necessary. The data will contribute to a better understanding of the biology of C. pseudotuberculosis and to studies investigating strategies to control the disease. Conclusions Despite the veterinary importance of C. pseudotuberculosis, the bacterium is poorly characterised; therefore, effective treatments for caseous lymphadenitis have been difficult to establish. Through the use of RNAseq, these results provide a better biological understanding of this bacterium, shed light on the most likely survival mechanisms used by this microorganism in adverse environments and identify candidates that may help reduce or even eradicate the problems caused by this disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Vasco Azevedo
- Department of General Biology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av, Antônio Carlos, Belo Horizonte 31,270-901, Brazil.
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Pereira UP, Soares SC, Blom J, Leal CAG, Ramos RTJ, Guimarães LC, Oliveira LC, Almeida SS, Hassan SS, Santos AR, Miyoshi A, Silva A, Tauch A, Barh D, Azevedo V, Figueiredo HCP. In silico prediction of conserved vaccine targets in Streptococcus agalactiae strains isolated from fish, cattle, and human samples. Genet Mol Res 2013; 12:2902-12. [PMID: 24065646 DOI: 10.4238/2013.august.12.6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Streptococcus agalactiae (Lancefield group B; group B streptococci) is a major pathogen that causes meningoencephalitis in fish, mastitis in cows, and neonatal sepsis and meningitis in humans. The available prophylactic measures for conserving human and animal health are not totally effective and have limitations. Effective vaccines against the different serotypes or genotypes of pathogenic strains from the various hosts would be useful. We used an in silico strategy to identify conserved vaccine candidates in 15 genomes of group B streptococci strains isolated from human, bovine, and fish samples. The degree of conservation, subcellular localization, and immunogenic potential of S. agalactiae proteins were investigated. We identified 36 antigenic proteins that were conserved in all 15 genomes. Among these proteins, 5 and 23 were shared only by human or fish strains, respectively. These potential vaccine targets may help develop effective vaccines that will help prevent S. agalactiae infection.
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Affiliation(s)
- U P Pereira
- AQUAVET - Laboratório de Doenças de Animais Aquáticos, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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20
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Castro TLP, Seyffert N, Ramos RTJ, Barbosa S, Carvalho RDO, Pinto AC, Carneiro AR, Silva WM, Pacheco LGC, Downson C, Schneider MPC, Miyoshi A, Azevedo V, Silva A. Ion Torrent-based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method. Microb Biotechnol 2013; 6:168-77. [PMID: 23316806 PMCID: PMC3917459 DOI: 10.1111/1751-7915.12020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/13/2012] [Accepted: 11/14/2012] [Indexed: 11/29/2022] Open
Abstract
Corynebacterium pseudotuberculosis equi is a Gram-positive pathogenic bacterium which affects a variety of hosts. Besides the great economic losses it causes to horse-breeders, this organism is also known to be an important infectious agent to cattle and buffaloes. As an outcome of the efforts in characterizing the molecular basis of its virulence, several complete genome sequences were made available in recent years, enabling the large-scale assessment of genes throughout distinct isolates. Meanwhile, the RNA-seq stood out as the technology of choice for comprehensive transcriptome studies, which may bring valuable information regarding active genomic regions, despite of the still impeditive associated costs. In an attempt to increase the use of generated reads per instrument run, by effectively eliminating unwanted rRNAs from total RNA samples without relying on any commercially available kits, we applied denaturing high-performance liquid chromatography (DHPLC) as an alternative method to assess the transcriptional profile of C. pseudotuberculosis. We have found that the DHPLC depletion method, allied to Ion Torrent sequencing, allows mapping of transcripts in a comprehensive way and identifying novel transcripts when a de novo approach is used. These data encourage us to use DHPLC in future transcriptional evaluations in C. pseudotuberculosis.
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Affiliation(s)
- Thiago L P Castro
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Nubia Seyffert
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Rommel T J Ramos
- Genome and Proteome Network of the State of Pará, Universidade Federal do ParáBrazil
| | - Silvanira Barbosa
- Genome and Proteome Network of the State of Pará, Universidade Federal do ParáBrazil
| | - Rodrigo D O Carvalho
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Anne Cybelle Pinto
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | | | - Wanderson Marques Silva
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Universidade Federal da BahiaSalvador, Brazil
| | | | - Maria P C Schneider
- Genome and Proteome Network of the State of Pará, Universidade Federal do ParáBrazil
| | - Anderson Miyoshi
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Universidade Federal de Minas GeraisBelo Horizonte, Brazil
| | - Artur Silva
- Genome and Proteome Network of the State of Pará, Universidade Federal do ParáBrazil
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21
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Soares SC, Trost E, Ramos RTJ, Carneiro AR, Santos AR, Pinto AC, Barbosa E, Aburjaile F, Ali A, Diniz CAA, Hassan SS, Fiaux K, Guimarães LC, Bakhtiar SM, Pereira U, Almeida SS, Abreu VAC, Rocha FS, Dorella FA, Miyoshi A, Silva A, Azevedo V, Tauch A. Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production. J Biotechnol 2012. [PMID: 23201561 DOI: 10.1016/j.jbiotec.2012.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Corynebacterium pseudotuberculosis is the causative agent of several veterinary diseases in a broad range of economically important hosts, which can vary from caseous lymphadenitis in sheep and goats (biovar ovis) to ulcerative lymphangitis in cattle and horses (biovar equi). Existing vaccines against C. pseudotuberculosis are mainly intended for small ruminants and, even in these hosts, they still present remarkable limitations. In this study, we present the complete genome sequence of C. pseudotuberculosis biovar equi strain 258, isolated from a horse with ulcerative lymphangitis. The genome has a total size of 2,314,404 bp and contains 2088 predicted protein-coding regions. Using in silico analysis, eleven pathogenicity islands were detected in the genome sequence of C. pseudotuberculosis 258. The application of a reverse vaccinology strategy identified 49 putative antigenic proteins, which can be used as candidate vaccine targets in future works.
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Affiliation(s)
- Siomar C Soares
- CLIB Graduate Cluster Industrial Biotechnology, Centrum für Biotechnologie, Universität Bielefeld, 33615 Bielefeld, Germany.
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22
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Ali A, Soares SC, Santos AR, Guimarães LC, Barbosa E, Almeida SS, Abreu VAC, Carneiro AR, Ramos RTJ, Bakhtiar SM, Hassan SS, Ussery DW, On S, Silva A, Schneider MP, Lage AP, Miyoshi A, Azevedo V. Campylobacter fetus subspecies: comparative genomics and prediction of potential virulence targets. Gene 2012; 508:145-56. [PMID: 22890137 DOI: 10.1016/j.gene.2012.07.070] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 07/30/2012] [Indexed: 01/10/2023]
Abstract
The genus Campylobacter contains pathogens causing a wide range of diseases, targeting both humans and animals. Among them, the Campylobacter fetus subspecies fetus and venerealis deserve special attention, as they are the etiological agents of human bacterial gastroenteritis and bovine genital campylobacteriosis, respectively. We compare the whole genomes of both subspecies to get insights into genomic architecture, phylogenetic relationships, genome conservation and core virulence factors. Pan-genomic approach was applied to identify the core- and pan-genome for both C. fetus subspecies and members of the genus. The C. fetus subspecies conserved (76%) proteome were then analyzed for their subcellular localization and protein functions in biological processes. Furthermore, with pathogenomic strategies, unique candidate regions in the genomes and several potential core-virulence factors were identified. The potential candidate factors identified for attenuation and/or subunit vaccine development against C. fetus subspecies contain: nucleoside diphosphate kinase (Ndk), type IV secretion systems (T4SS), outer membrane proteins (OMP), substrate binding proteins CjaA and CjaC, surface array proteins, sap gene, and cytolethal distending toxin (CDT). Significantly, many of those genes were found in genomic regions with signals of horizontal gene transfer and, therefore, predicted as putative pathogenicity islands. We found CRISPR loci and dam genes in an island specific for C. fetus subsp. fetus, and T4SS and sap genes in an island specific for C. fetus subsp. venerealis. The genomic variations and potential core and unique virulence factors characterized in this study would lead to better insight into the species virulence and to more efficient use of the candidates for antibiotic, drug and vaccine development.
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Affiliation(s)
- Amjad Ali
- Federal University of Minas Gerais, Belo Horizonte, 31907-270, Minas Gerais, Brazil.
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23
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Soares SC, Abreu VAC, Ramos RTJ, Cerdeira L, Silva A, Baumbach J, Trost E, Tauch A, Hirata R, Mattos-Guaraldi AL, Miyoshi A, Azevedo V. PIPS: pathogenicity island prediction software. PLoS One 2012; 7:e30848. [PMID: 22355329 PMCID: PMC3280268 DOI: 10.1371/journal.pone.0030848] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 12/22/2011] [Indexed: 01/08/2023] Open
Abstract
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.
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Affiliation(s)
- Siomar C. Soares
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vinícius A. C. Abreu
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Louise Cerdeira
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Artur Silva
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Jan Baumbach
- Department of Computer Science, Max-Planck-Institut für Informatik, Saarbrücken, Saarland, Germany
| | - Eva Trost
- Center for Biotechnology, Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany
| | - Andreas Tauch
- Center for Biotechnology, Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany
| | - Raphael Hirata
- Microbiology and Immunology Discipline, Medical Sciences Faculty, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana L. Mattos-Guaraldi
- Microbiology and Immunology Discipline, Medical Sciences Faculty, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anderson Miyoshi
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
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24
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Pinto AC, Ramos RTJ, Silva WM, Rocha FS, Barbosa S, Miyoshi A, Schneider MPC, Silva A, Azevedo V. The core stimulon of Corynebacterium pseudotuberculosis strain 1002 identified using ab initio methodologies. Integr Biol (Camb) 2012; 4:789-94. [DOI: 10.1039/c2ib00092j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Ruiz JC, D'Afonseca V, Silva A, Ali A, Pinto AC, Santos AR, Rocha AAMC, Lopes DO, Dorella FA, Pacheco LGC, Costa MP, Turk MZ, Seyffert N, Moraes PMRO, Soares SC, Almeida SS, Castro TLP, Abreu VAC, Trost E, Baumbach J, Tauch A, Schneider MPC, McCulloch J, Cerdeira LT, Ramos RTJ, Zerlotini A, Dominitini A, Resende DM, Coser EM, Oliveira LM, Pedrosa AL, Vieira CU, Guimarães CT, Bartholomeu DC, Oliveira DM, Santos FR, Rabelo ÉM, Lobo FP, Franco GR, Costa AF, Castro IM, Dias SRC, Ferro JA, Ortega JM, Paiva LV, Goulart LR, Almeida JF, Ferro MIT, Carneiro NP, Falcão PRK, Grynberg P, Teixeira SMR, Brommonschenkel S, Oliveira SC, Meyer R, Moore RJ, Miyoshi A, Oliveira GC, Azevedo V. Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains. PLoS One 2011; 6:e18551. [PMID: 21533164 PMCID: PMC3078919 DOI: 10.1371/journal.pone.0018551] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 03/11/2011] [Indexed: 02/02/2023] Open
Abstract
Background Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity. Methodology and Findings We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in genomic architecture, gene content and genetic order. When C. pseudotuberculosis was compared with other Corynebacterium species, it became evident that this pathogenic species has lost numerous genes, resulting in one of the smallest genomes in the genus. Other differences that could be part of the adaptation to pathogenicity include a lower GC content, of about 52%, and a reduced gene repertoire. The C. pseudotuberculosis genome also includes seven putative pathogenicity islands, which contain several classical virulence factors, including genes for fimbrial subunits, adhesion factors, iron uptake and secreted toxins. Additionally, all of the virulence factors in the islands have characteristics that indicate horizontal transfer. Conclusions These particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenicity pathways used by this pathogen in the infection process. All genomes cited in this study are available in the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers CP001809 and CP001829.
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Affiliation(s)
- Jerônimo C. Ruiz
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Vívian D'Afonseca
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Amjad Ali
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anne C. Pinto
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anderson R. Santos
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aryanne A. M. C. Rocha
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Débora O. Lopes
- Health Sciences Center, Federal University of São João Del Rei, Divinópilis, Minas Gerais, Brazil
| | - Fernanda A. Dorella
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luis G. C. Pacheco
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Biointeraction Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Marcília P. Costa
- Department of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Meritxell Z. Turk
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Núbia Seyffert
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Pablo M. R. O. Moraes
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Siomar C. Soares
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sintia S. Almeida
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thiago L. P. Castro
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vinicius A. C. Abreu
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eva Trost
- Department of Genetics, University of Bielefeld, CeBiTech, Bielefeld, Nordrhein-Westfale, Germany
| | - Jan Baumbach
- Department of Computer Science, Max-Planck-Institut für Informatik, Saarbrücken, Saarlan, Germany
| | - Andreas Tauch
- Department of Genetics, University of Bielefeld, CeBiTech, Bielefeld, Nordrhein-Westfale, Germany
| | | | - John McCulloch
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | | | | | - Adhemar Zerlotini
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Anderson Dominitini
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Daniela M. Resende
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
- Department of Pharmaceutical Sciences, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Elisângela M. Coser
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Luciana M. Oliveira
- Department of Phisics, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - André L. Pedrosa
- Department of Pharmaceutical Sciences, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
- Department of Biological Sciences, Federal University of Triangulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Carlos U. Vieira
- Department of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Cláudia T. Guimarães
- Brazilian Agricultural Research Corporation (EMBRAPA), Sete Lagoas, Minas Gerais, Brazil
| | - Daniela C. Bartholomeu
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Diana M. Oliveira
- Department of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Fabrício R. Santos
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Élida Mara Rabelo
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francisco P. Lobo
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glória R. Franco
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Flávia Costa
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ieso M. Castro
- Department of Pharmacy, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Sílvia Regina Costa Dias
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jesus A. Ferro
- Department of Technology, State University of São Paulo, Jaboticabal, São Paulo, Brazil
| | - José Miguel Ortega
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luciano V. Paiva
- Department of Chemistry, Federal University of Lavras, Lavras, Minas Gerais, Brazil
| | - Luiz R. Goulart
- Department of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Juliana Franco Almeida
- Department of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Maria Inês T. Ferro
- Department of Technology, State University of São Paulo, Jaboticabal, São Paulo, Brazil
| | - Newton P. Carneiro
- Brazilian Agricultural Research Corporation (EMBRAPA), Sete Lagoas, Minas Gerais, Brazil
| | - Paula R. K. Falcão
- Brazilian Agricultural Research Corporation (EMBRAPA), Campinas, São Paulo, Brazil
| | - Priscila Grynberg
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Santuza M. R. Teixeira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sérgio Brommonschenkel
- Department of Plant Pathology, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Sérgio C. Oliveira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roberto Meyer
- Department of Biointeraction Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | - Anderson Miyoshi
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Guilherme C. Oliveira
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
- Center of Excellence in Bioinformatics, National Institute of Science and Technology, Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
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