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Gomes LGR, Dutra JCF, Profeta R, Dias MV, García GJY, Rodrigues DLN, Goés Neto A, Aburjaile FF, Tiwari S, Soares SC, Azevedo V, Jaiswal AK. Systematic review of reverse vaccinology and immunoinformatics data for non-viral sexually transmitted infections. AN ACAD BRAS CIENC 2023; 95:e20230617. [PMID: 38055447 DOI: 10.1590/0001-3765202320230617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/27/2023] [Indexed: 12/08/2023] Open
Abstract
Sexually Transmitted Infections (STIs) are a public health burden rising in developed and developing nations. The World Health Organization estimates nearly 374 million new cases of curable STIs yearly. Global efforts to control their spread have been insufficient in fulfilling their objective. As there is no vaccine for many of these infections, these efforts are focused on education and condom distribution. The development of vaccines for STIs is vital for successfully halting their spread. The field of immunoinformatics is a powerful new tool for vaccine development, allowing for the identification of vaccine candidates within a bacterium's genome and allowing for the design of new genome-based vaccine peptides. The goal of this review was to evaluate the usage of immunoinformatics in research focused on non-viral STIs, identifying fields where research efforts are concentrated. Here we describe gaps in applying these techniques, as in the case of Treponema pallidum and Trichomonas vaginalis.
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Affiliation(s)
- Lucas Gabriel R Gomes
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Joyce C F Dutra
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Microbiologia, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Rodrigo Profeta
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Mariana V Dias
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Glen J Y García
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Bioinformática, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Diego Lucas N Rodrigues
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal de Minas Gerais (UFMG), Escola de Veterinária, Departamento de Medicina Veterinária, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Aristóteles Goés Neto
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Microbiologia, Laboratório de Biologia Molecular e Computacional de Fungos, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Flávia F Aburjaile
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal de Minas Gerais (UFMG), Escola de Veterinária, Departamento de Medicina Veterinária, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal da Bahia, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, Ondina, 40170-115 Salvador, BA, Brazil
- Universidade Federal da Bahia, Instituto de Ciências da Saúde, Av. Reitor Miguel Calmon, s/n, Vale do Canela, 40110-902 Salvador, BA, Brazil
| | - Siomar C Soares
- Universidade Federal do Triângulo Mineiro (UFTM), Instituto de Ciências Biológicas e Naturais, Departamento de Microbiologia, Imunologia, e Parasitologia, Rua Vigário Carlos, 100, Abadia, 38025-180 Uberaba, MG, Brazil
| | - Vasco Azevedo
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Arun K Jaiswal
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
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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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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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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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5
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Jaiswal AK, Tiwari S, Jamal SB, Oliveira LDC, Sales-Campos H, Andrade-Silva LE, Oliveira CJF, Ghosh P, Barh D, Azevedo V, Soares SC, Rodrigues VR, da Silva MV. Reverse vaccinology and subtractive genomics approaches for identifying common therapeutics against Mycobacterium leprae and Mycobacterium lepromatosis. J Venom Anim Toxins Incl Trop Dis 2021; 27:e20200027. [PMID: 33889182 PMCID: PMC8040911 DOI: 10.1590/1678-9199-jvatitd-2020-0027] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 12/09/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Mycobacterium leprae and Mycobacterium lepromatosis are gram-positive bacterial pathogens and the causative agents of leprosy in humans across the world. The elimination of leprosy cannot be achieved by multidrug therapy alone, and highlights the need for new tools and drugs to prevent the emergence of new resistant strains. METHODS In this study, our contribution includes the prediction of vaccine targets and new putative drugs against leprosy, using reverse vaccinology and subtractive genomics. Six strains of Mycobacterium leprae and Mycobacterium lepromatosis (4 and 2 strains, respectively) were used for comparison taking Mycobacterium leprae strain TN as the reference genome. Briefly, we used a combined reverse vaccinology and subtractive genomics approach. RESULTS As a result, we identified 12 common putative antigenic proteins as vaccine targets and three common drug targets against Mycobacterium leprae and Mycobacterium lepromatosis. Furthermore, the docking analysis using 28 natural compounds with three drug targets was done. CONCLUSIONS The bis-naphthoquinone compound Diospyrin (CID 308140) obtained from indigenous plant Diospyros spp. showed the most favored binding affinity against predicted drug targets, which can be a candidate therapeutic target in the future against leprosy.
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Affiliation(s)
- Arun Kumar Jaiswal
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Sandeep Tiwari
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Punjab, Pakistan
| | - Letícia de Castro Oliveira
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Helioswilton Sales-Campos
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
- Institute of Tropical Pathology and Public Health, Federal University of Goias (UFG), Goiânia, Goiás, Brazil
| | - Leonardo Eurípedes Andrade-Silva
- Infectious Disease Department, Institute of Health Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Carlo Jose Freire Oliveira
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Preetam Ghosh
- 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, Purba Medinipur, West Bengal, India
| | - Vasco Azevedo
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Siomar C. Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Virmondes Rodrigues Rodrigues
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Marcos Vinicius da Silva
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
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Jaiswal AK, Tiwari S, Jamal SB, de Castro Oliveira L, Alves LG, Azevedo V, Ghosh P, Oliveira CJF, Soares SC. The pan-genome of Treponema pallidum reveals differences in genome plasticity between subspecies related to venereal and non-venereal syphilis. BMC Genomics 2020; 21:33. [PMID: 31924165 PMCID: PMC6953169 DOI: 10.1186/s12864-019-6430-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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] [Received: 10/10/2019] [Accepted: 12/24/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Spirochetal organisms of the Treponema genus are responsible for causing Treponematoses. Pathogenic treponemes is a Gram-negative, motile, spirochete pathogen that causes syphilis in human. Treponema pallidum subsp. endemicum (TEN) causes endemic syphilis (bejel); T. pallidum subsp. pallidum (TPA) causes venereal syphilis; T. pallidum subsp. pertenue (TPE) causes yaws; and T. pallidum subsp. Ccarateum causes pinta. Out of these four high morbidity diseases, venereal syphilis is mediated by sexual contact; the other three diseases are transmitted by close personal contact. The global distribution of syphilis is alarming and there is an increasing need of proper treatment and preventive measures. Unfortunately, effective measures are limited. RESULTS Here, the genome sequences of 53 T. pallidum strains isolated from different parts of the world and a diverse range of hosts were comparatively analysed using pan-genomic strategy. Phylogenomic, pan-genomic, core genomic and singleton analysis disclosed the close connection among all strains of the pathogen T. pallidum, its clonal behaviour and showed increases in the sizes of the pan-genome. Based on the genome plasticity analysis of the subsets containing the subspecies T pallidum subsp. pallidum, T. pallidum subsp. endemicum and T. pallidum subsp. pertenue, we found differences in the presence/absence of pathogenicity islands (PAIs) and genomic islands (GIs) on subsp.-based study. CONCLUSIONS In summary, we identified four pathogenicity islands (PAIs), eight genomic islands (GIs) in subsp. pallidum, whereas subsp. endemicum has three PAIs and seven GIs and subsp. pertenue harbours three PAIs and eight GIs. Concerning the presence of genes in PAIs and GIs, we found some genes related to lipid and amino acid biosynthesis that were only present in the subsp. of T. pallidum, compared to T. pallidum subsp. endemicum and T. pallidum subsp. pertenue.
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Affiliation(s)
- Arun Kumar Jaiswal
- PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.,Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Sandeep Tiwari
- PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Abid Majeed Road, Rawalpindi, Punjab, 46000, Pakistan
| | - Letícia de Castro Oliveira
- PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.,Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Leandro Gomes Alves
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Vasco Azevedo
- PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA-23284, USA
| | - Carlo Jose Freira Oliveira
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Siomar C Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil.
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7
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Tosta SFDO, Passos MS, Kato R, Salgado Á, Xavier J, Jaiswal AK, Soares SC, Azevedo V, Giovanetti M, Tiwari S, Alcantara LCJ. Multi-epitope based vaccine against yellow fever virus applying immunoinformatics approaches. J Biomol Struct Dyn 2020; 39:219-235. [PMID: 31854239 DOI: 10.1080/07391102.2019.1707120] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 01/08/2023]
Abstract
Yellow fever disease is considered a re-emerging major health issue which has caused recent outbreaks with a high number of deaths. Tropical countries, mainly African and South American, are the most affected by Yellow fever outbreaks. Despite the availability of an attenuated vaccine, its use is limited for some groups such as pregnant and nursing women, immunocompromised and immunosuppressed patients, elderly people >65 years, infants <6 months and patients with biological disorders like thymus disorders. In order to achieve new preventive measures, we applied immunoinformatics approaches to develop a multi-epitope-based subunit vaccine for Yellow fever virus. Different epitopes, related to humoral and cell-mediated immunity, were predicted for complete polyproteins of two Yellow fever strains (Asibi and 17 D vaccine). Those epitopes common for both strains were mapped into a set of 137 sequences of Yellow fever virus, including 77 sequences from a recent outbreak at the state of Minas Gerais, southeast Brazil. Therefore, the present work uses robust bioinformatics approaches for the identification of a multi-epitope vaccine against the Yellow fever virus. Our results indicate that the identified multi-epitope vaccine might stimulate humoral and cellular immune responses and could be a potential vaccine candidate against Yellow fever virus infection. Hence, it should be subjected to further experimental validations. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Stephane Fraga de Oliveira Tosta
- Postgraduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Mariana Santana Passos
- Department of Genetics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Rodrigo Kato
- Postgraduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Álvaro Salgado
- Postgraduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Joilson Xavier
- Department of Genetics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Arun Kumar Jaiswal
- Postgraduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.,Department of Immunology, Microbiology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Siomar C Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil
| | - Vasco Azevedo
- Postgraduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Marta Giovanetti
- Department of Genetics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.,Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Manguinhos, Rio De Janeiro, Brazil
| | - Sandeep Tiwari
- Postgraduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Luiz Carlos Junior Alcantara
- Department of Genetics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.,Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Manguinhos, Rio De Janeiro, Brazil
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8
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Silva WM, Sousa CS, Oliveira LC, Soares SC, Souza GFMH, Tavares GC, Resende CP, Folador EL, Pereira FL, Figueiredo H, Azevedo V. Comparative proteomic analysis of four biotechnological strains Lactococcus lactis through label-free quantitative proteomics. Microb Biotechnol 2018; 12:265-274. [PMID: 30341804 PMCID: PMC6389847 DOI: 10.1111/1751-7915.13305] [Citation(s) in RCA: 11] [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: 11/09/2017] [Revised: 06/25/2018] [Accepted: 07/21/2018] [Indexed: 12/12/2022] Open
Abstract
Lactococcus lactis is a bacteria with high biotechnological potential, where is frequently used in the amino acid production and production of fermented dairy products, as well as drug delivery systems and mucosal vaccine vector. The knowledge of a functional core proteome is important extremely for both fundamental understanding of cell functions and for synthetic biology applications. In this study, we characterized the L. lacits proteome from proteomic analysis of four biotechnological strains L. lactis: L. lactis subsp. lactis NCDO2118, L. lactis subsp. lactis IL1403, L. lactis subsp. cremoris NZ9000 and L. lactis subsp. cremoris MG1363. Our label‐free quantitative proteomic analysis of the whole bacterial lysates from each strains resulted in the characterization of the L. lactis core proteome that was composed by 586 proteins, which might contribute to resistance of this bacterium to different stress conditions as well as involved in the probiotic characteristic of L. lactis. Kegg enrichment analysis shows that ribosome, metabolic pathways, pyruvate metabolism and microbial metabolism in diverse environments were the most enriched. According to our quantitative proteomic analysis, proteins related to translation process were the more abundant in the core proteome, which represent an important step in the synthetic biology. In addition, we identified a subset of conserved proteins that are exclusive of the L. lactis subsp. cremoris or L. lactis subsp. lactis, which some are related to metabolic pathway exclusive. Regarding specific proteome of NCDO2118, we detected ‘strain‐specific proteins’. Finally, proteogenomics analysis allows the identification of proteins, which were not previously annotated in IL1403 and MG1363. The results obtained in this study allowed to increase our knowledge about the biology of L. lactis, which contributes to the implementation of strategies that make it possible to increase the biotechnological potential of this bacterium.
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Affiliation(s)
- Wanderson M Silva
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Cassiana S Sousa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Leticia C Oliveira
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil.,Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Naturais e Biológicas, Universidade Federal do Triangulo Mineiro, Uberaba, Minas Gerais, Brasil
| | - Siomar C Soares
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Naturais e Biológicas, Universidade Federal do Triangulo Mineiro, Uberaba, Minas Gerais, Brasil
| | - Gustavo F M H Souza
- MS Applications Laboratory, Waters Corporation, Waters Technologies Brazil, Alphaville, São Paulo, Brasil
| | - Guilherme C Tavares
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Cristiana P Resende
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Edson L Folador
- Centro de Biotecnologia, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brasil
| | - Felipe L Pereira
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Henrique Figueiredo
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Vasco Azevedo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
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9
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Nevoa JC, Mendes MT, da Silva MV, Soares SC, Oliveira CJF, Ribeiro JMC. An insight into the salivary gland and fat body transcriptome of Panstrongylus lignarius (Hemiptera: Heteroptera), the main vector of Chagas disease in Peru. PLoS Negl Trop Dis 2018; 12:e0006243. [PMID: 29462134 PMCID: PMC5834209 DOI: 10.1371/journal.pntd.0006243] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 11/08/2017] [Revised: 03/02/2018] [Accepted: 01/17/2018] [Indexed: 12/31/2022] Open
Abstract
Triatomines are hematophagous arthropod vectors of Trypanosoma cruzi, the causative agent of Chagas Disease. Panstrongylus lignarius, also known as Panstrongylus herreri, is considered one of the most versatile triatomines because it can parasitize different hosts, it is found in different habitats and countries, it has sylvatic, peridomestic and domestic behavior and it is a very important vector of Chagas disease, especially in Peru. Molecules produced and secreted by salivary glands and fat body are considered of important adaptational value for triatomines because, among other functions, they subvert the host haemostatic, inflammatory and immune systems and detoxify or protect them against environmental aggressors. In this context, the elucidation of the molecules produced by these tissues is highly valuable to understanding the ability of this species to adapt and transmit pathogens. Here, we use high-throughput sequencing techniques to assemble and describe the coding sequences resulting from the transcriptome of the fat body and salivary glands of P. lignarius. The final assembly of both transcriptomes together resulted in a total of 11,507 coding sequences (CDS), which were mapped from a total of 164,676,091 reads. The CDS were subdivided according to their 10 folds overexpression on salivary glands (513 CDS) or fat body (2073 CDS). Among the families of proteins found in the salivary glands, lipocalins were the most abundant. Other ubiquitous families of proteins present in other sialomes were also present in P. lignarius, including serine protease inhibitors, apyrase and antigen-5. The unique transcriptome of fat body showed proteins related to the metabolic function of this organ. Remarkably, nearly 20% of all reads mapped to transcripts coded by Triatoma virus. The data presented in this study improve the understanding on triatomines' salivary glands and fat body function and reveal important molecules used in the interplay between vectors and vertebrate hosts.
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Affiliation(s)
- Jessica C. Nevoa
- Institute of Natural and Biological Sciences, Laboratory of Immunology, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Maria T. Mendes
- University of Texas at El Paso, El Paso, Texas, United States of America
| | - Marcos V. da Silva
- Institute of Natural and Biological Sciences, Laboratory of Immunology, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Siomar C. Soares
- Institute of Natural and Biological Sciences, Laboratory of Immunology, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Carlo J. F. Oliveira
- Institute of Natural and Biological Sciences, Laboratory of Immunology, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - José M. C. Ribeiro
- National Institute of Allergy and Infectious Diseases (NIAID), Laboratory of Malaria and Vector Research (LMVR), Rockville, Maryland, United States of America
- * E-mail:
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10
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Silva WM, Folador EL, Soares SC, Souza GHMF, Santos AV, Sousa CS, Figueiredo H, Miyoshi A, Le Loir Y, Silva A, Azevedo V. Label-free quantitative proteomics of Corynebacterium pseudotuberculosis isolates reveals differences between Biovars ovis and equi strains. BMC Genomics 2017; 18:451. [PMID: 28595597 PMCID: PMC5463331 DOI: 10.1186/s12864-017-3835-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 05/31/2017] [Indexed: 11/24/2022] Open
Affiliation(s)
- Wanderson M Silva
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil.,INRA, UMR1253 STLO, 35042, Rennes, France.,Agrocampus Ouest, UMR1253 STLO, 35042, Rennes, France
| | - Edson L Folador
- Centro de Biotecnologia, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brasil
| | - Siomar C Soares
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil.,Departmento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brasil
| | - Gustavo H M F Souza
- Waters Corporation, Waters Technologies Brazil, MS Applications Laboratory, Alphaville, São Paulo, Brasil
| | - Agenor V Santos
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Cassiana S Sousa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Henrique Figueiredo
- Escola de Veterinária, Aquavet, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Anderson Miyoshi
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Yves Le Loir
- INRA, UMR1253 STLO, 35042, Rennes, France.,Agrocampus Ouest, UMR1253 STLO, 35042, Rennes, France
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Vasco Azevedo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil.
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11
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Oliveira LC, Saraiva TDL, Silva WM, Pereira UP, Campos BC, Benevides LJ, Rocha FS, Figueiredo HCP, Azevedo V, Soares SC. Analyses of the probiotic property and stress resistance-related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays. PLoS One 2017; 12:e0175116. [PMID: 28384209 PMCID: PMC5383145 DOI: 10.1371/journal.pone.0175116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 11/14/2016] [Accepted: 03/21/2017] [Indexed: 11/19/2022] Open
Abstract
Lactococcus lactis subsp. lactis NCDO 2118 was recently reported to alleviate colitis symptoms via its anti-inflammatory and immunomodulatory activities, which are exerted by exported proteins that are not produced by L. lactis subsp. lactis IL1403. Here, we used in vitro and in silico approaches to characterize the genomic structure, the safety aspects, and the immunomodulatory activity of this strain. Through comparative genomics, we identified genomic islands, phage regions, bile salt and acid stress resistance genes, bacteriocins, adhesion-related and antibiotic resistance genes, and genes encoding proteins that are putatively secreted, expressed in vitro and absent from IL1403. The high degree of similarity between all Lactococcus suggests that the Symbiotic Islands commonly shared by both NCDO 2118 and KF147 may be responsible for their close relationship and their adaptation to plants. The predicted bacteriocins may play an important role against the invasion of competing strains. The genes related to the acid and bile salt stresses may play important roles in gastrointestinal tract survival, whereas the adhesion proteins are important for persistence in the gut, culminating in the competitive exclusion of other bacteria. Finally, the five secreted and expressed proteins may be important targets for studies of new anti-inflammatory and immunomodulatory proteins. Altogether, the analyses performed here highlight the potential use of this strain as a target for the future development of probiotic foods.
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Affiliation(s)
- Letícia C. Oliveira
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Tessália D. L. Saraiva
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Wanderson M. Silva
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Ulisses P. Pereira
- Department of Preventive Veterinary Medicine, State University of Londrina, Londrina—PR, Brazil
| | - Bruno C. Campos
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Leandro J. Benevides
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Flávia S. Rocha
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Henrique C. P. Figueiredo
- Official Laboratory of Fisheries Ministry—Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
| | - Siomar C. Soares
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte—MG, Brazil
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba—MG, Brazil
- * E-mail:
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12
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Silva WM, Dorella FA, Soares SC, Souza GHMF, Castro TLP, Seyffert N, Figueiredo H, Miyoshi A, Le Loir Y, Silva A, Azevedo V. A shift in the virulence potential of Corynebacterium pseudotuberculosis biovar ovis after passage in a murine host demonstrated through comparative proteomics. BMC Microbiol 2017; 17:55. [PMID: 28327085 PMCID: PMC5361795 DOI: 10.1186/s12866-017-0925-6] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 01/04/2017] [Indexed: 01/19/2023] Open
Abstract
Background Corynebacterium pseudotuberculosis biovar ovis, a facultative intracellular pathogen, is the etiologic agent of caseous lymphadenitis in small ruminants. During the infection process, C. pseudotuberculosis changes its gene expression to resist different types of stresses and to evade the immune system of the host. However, factors contributing to the infectious process of this pathogen are still poorly documented. To better understand the C. pseudotuberculosis infection process and to identify potential factors which could be involved in its virulence, experimental infection was carried out in a murine model using the strain 1002_ovis and followed by a comparative proteomic analysis of the strain before and after passage. Results The experimental infection assays revealed that strain 1002_ovis exhibits low virulence potential. However, the strain recovered from the spleen of infected mice and used in a new infection challenge showed a dramatic change in its virulence potential. Label-free proteomic analysis of the culture supernatants of strain 1002_ovis before and after passage in mice revealed that 118 proteins were differentially expressed. The proteome exclusive to the recovered strain contained important virulence factors such as CP40 proteinase and phospholipase D exotoxin, the major virulence factor of C. pseudotuberculosis. Also, the proteome from recovered condition revealed different classes of proteins involved in detoxification processes, pathogenesis and export pathways, indicating the presence of distinct mechanisms that could contribute in the infectious process of this pathogen. Conclusions This study shows that C. pseudotuberculosis modifies its proteomic profile in the laboratory versus infection conditions and adapts to the host context during the infection process. The screening proteomic performed us enable identify known virulence factors, as well as potential proteins that could be related to virulence this pathogen. These results enhance our understanding of the factors that might influence in the virulence of C. pseudotuberculosis. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0925-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wanderson M Silva
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,INRA, UMR1253 STLO, 35042, Rennes, France.,Agrocampus Ouest, UMR1253 STLO, 35042, Rennes, France
| | - Fernanda A Dorella
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Siomar C Soares
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gustavo H M F Souza
- Waters Corporation, Waters Technologies Brazil, MS Applications Laboratory, Alphaville, São Paulo, Brazil
| | - Thiago L P Castro
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Núbia Seyffert
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Henrique Figueiredo
- Aquacen, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Anderson Miyoshi
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Yves Le Loir
- INRA, UMR1253 STLO, 35042, Rennes, France.,Agrocampus Ouest, UMR1253 STLO, 35042, Rennes, France
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Guamá, Belém, Pará, Brazil
| | - Vasco Azevedo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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13
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Soares SC, Geyik H, Ramos RT, de Sá PH, Barbosa EG, Baumbach J, Figueiredo HC, Miyoshi A, Tauch A, Silva A, Azevedo V. GIPSy: Genomic island prediction software. J Biotechnol 2016; 232:2-11. [DOI: 10.1016/j.jbiotec.2015.09.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/28/2015] [Accepted: 09/11/2015] [Indexed: 10/23/2022]
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Pereira FL, Soares SC, Dorella FA, Leal CA, Figueiredo HC. Evaluating the efficacy of the new Ion PGM Hi-Q Sequencing Kit applied to bacterial genomes. Genomics 2016; 107:189-98. [DOI: 10.1016/j.ygeno.2016.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/01/2016] [Accepted: 03/17/2016] [Indexed: 11/28/2022]
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15
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Figueiredo HCP, Soares SC, Pereira FL, Dorella FA, Carvalho AF, Teixeira JP, Azevedo VAC, Leal CAG. Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout. BMC Genomics 2015; 16:1095. [PMID: 26694728 PMCID: PMC4687380 DOI: 10.1186/s12864-015-2324-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 06/25/2015] [Accepted: 12/15/2015] [Indexed: 11/10/2022] Open
Abstract
Background The genus Weissella belongs to the lactic acid bacteria and includes 18 currently identified species, predominantly isolated from fermented food but rarely from cases of bacteremia in animals. Recently, a new species, designated Weissella ceti, has been correlated with hemorrhagic illness in farm-raised rainbow trout in China, Brazil, and the USA, with high transmission and mortality rates during outbreaks. Although W. ceti is an important emerging veterinary pathogen, little is known about its genomic features or virulence mechanisms. To better understand these and to characterize the species, we have previously sequenced the genomes of W. ceti strains WS08, WS74, and WS105, isolated from different rainbow trout farms in Brazil and displaying different pulsed-field gel electrophoresis patterns. Here, we present a comparative analysis of the three previously sequenced genomes of W. ceti strains from Brazil along with W. ceti NC36 from the USA and those of other Weissella species. Results Phylogenomic and orthology-based analyses both showed a high-similarity in the genetic structure of these W. ceti strains. This structure is corroborated by the highly syntenic order of their genes and the neutral evolution inferred from Tajima’s D. A whole-genome multilocus sequence typing analysis distinguished strains WS08 and NC36 from strains WS74 and WS105. We predicted 10 putative genomic islands (GEI), among which PAIs 3a and 3b are phage sequences that occur only in WS105 and WS74, respectively, whereas PAI 1 is species specific. Conclusions We identified several genes putatively involved in the basic processes of bacterial physiology and pathogenesis, including survival in aquatic environment, adherence in the host, spread inside the host, resistance to immune-system-mediated stresses, and antibiotic resistance. These data provide new insights in the molecular epidemiology and host adaptation for this emerging pathogen in aquaculture. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2324-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Henrique C P Figueiredo
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Veterinary School, Department of Preventive Veterinary Medicine, Federal University of Minas Gerais, Av. Antônio Carlos 6627, Pampulha, Belo Horizonte, 30161-970, MG, Brazil.
| | - Siomar C Soares
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Felipe L Pereira
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Fernanda A Dorella
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Alex F Carvalho
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Júnia P Teixeira
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Vasco A C Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute for Biological Science, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Carlos A G Leal
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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16
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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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17
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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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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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19
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Soares SC, Silva A, Trost E, Blom J, Ramos R, Carneiro A, Ali A, Santos AR, Pinto AC, Diniz C, Barbosa EGV, Dorella FA, Aburjaile F, Rocha FS, Nascimento KKF, Guimarães LC, Almeida S, Hassan SS, Bakhtiar SM, Pereira UP, Abreu VAC, Schneider MPC, Miyoshi A, Tauch A, Azevedo V. The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains. PLoS One 2013; 8:e53818. [PMID: 23342011 PMCID: PMC3544762 DOI: 10.1371/journal.pone.0053818] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [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: 10/08/2012] [Accepted: 12/03/2012] [Indexed: 12/11/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a facultative intracellular pathogen and the causative agent of several infectious and contagious chronic diseases, including caseous lymphadenitis, ulcerative lymphangitis, mastitis, and edematous skin disease, in a broad spectrum of hosts. In addition, Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic, and singleton analyses revealed close relationships among pathogenic corynebacteria, the clonal-like behavior of C. pseudotuberculosis and slow increases in the sizes of pan-genomes. According to extrapolations based on the pan-genomes, core genomes and singletons, the C. pseudotuberculosis biovar ovis shows a more clonal-like behavior than the C. pseudotuberculosis biovar equi. Most of the variable genes of the biovar ovis strains were acquired in a block through horizontal gene transfer and are highly conserved, whereas the biovar equi strains contain great variability, both intra- and inter-biovar, in the 16 detected pathogenicity islands (PAIs). With respect to the gene content of the PAIs, the most interesting finding is the high similarity of the pilus genes in the biovar ovis strains compared with the great variability of these genes in the biovar equi strains. Concluding, the polymerization of complete pilus structures in biovar ovis could be responsible for a remarkable ability of these strains to spread throughout host tissues and penetrate cells to live intracellularly, in contrast with the biovar equi, which rarely attacks visceral organs. Intracellularly, the biovar ovis strains are expected to have less contact with other organisms than the biovar equi strains, thereby explaining the significant clonal-like behavior of the biovar ovis strains.
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Affiliation(s)
- Siomar C. Soares
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Center for Biotechnology, Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany
- CLIB Graduate Cluster Industrial Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany
| | - Artur Silva
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Eva Trost
- Center for Biotechnology, Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany
- CLIB Graduate Cluster Industrial Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany
| | - Jochen Blom
- Center for Biotechnology, Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany
| | - Rommel Ramos
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Adriana Carneiro
- 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
| | - Anderson R. Santos
- 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
| | - Carlos Diniz
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eudes G. V. Barbosa
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda A. Dorella
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Flávia Aburjaile
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Flávia S. Rocha
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Karina K. F. Nascimento
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luís C. Guimarães
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Center for Biotechnology, Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany
- CLIB Graduate Cluster Industrial Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany
| | - Sintia Almeida
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Syed S. Hassan
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Syeda M. Bakhtiar
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ulisses P. Pereira
- Department of Veterinary Medicine, Federal University of Lavras, Lavras, Brazil
| | - Vinicius A. C. Abreu
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Anderson Miyoshi
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Andreas Tauch
- Center for Biotechnology, Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany
| | - Vasco Azevedo
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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20
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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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21
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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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22
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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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23
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Soares SC, Dorella FA, Pacheco LGC, Hirata R, Mattos-Guaraldi AL, Azevedo V, Miyoshi A. Plasticity of Corynebacterium diphtheriae pathogenicity islands revealed by PCR. Genet Mol Res 2011; 10:1290-4. [PMID: 21732292 DOI: 10.4238/vol10-2gmr1211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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
Despite the existence of a vaccine against diphtheria, this disease remains endemic and is reemerging in several regions due to many factors, including variations in genes coding for virulence factors. One common feature of virulence factors is their high concentration in pathogenicity islands (PAIs), very unstable regions acquired via horizontal gene transfer, which has lead to the emergence of various bacterial pathogens. The 13 putative PAIs in Corynebacterium diphtheriae NCTC 13129 and the reemergence of this disease point to the great variability in the PAIs of this species, which may reflect on bacterial life style and physiological versatility. We investigated the relationships between the large number of PAIs in C. diphtheriae and the possible implications of their plasticity in virulence. The GenoFrag software was used to design primers to analyze the genome plasticity of two pathogenicity islands of the reference strain (PiCds 3 and 8) in 11 different strains. We found that PiCd 3 was absent in only two strains, showing genes playing putative important roles in virulence and that only one strain harbored PiCd 8, due to its location in a putative "hotspot" for horizontal gene transfer events.
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Affiliation(s)
- S C Soares
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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24
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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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Soares SC, Abé-Sandes K, Nascimento Filho VB, Nunes FMF, Silva WA. Genetic polymorphisms in TLR4, CR1 and Duffy genes are not associated with malaria resistance in patients from Baixo Amazonas region, Brazil. Genet Mol Res 2008; 7:1011-9. [PMID: 19048480 DOI: 10.4238/vol7-4gmr439] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [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
The main purpose of this research was to analyze the relation of the genetic polymorphisms frequently expressed by antigen-presenting cells, erythrocytes and malaria susceptibility/resistance with the human malaria infection cases. The sample used consisted of 23 Plasmodium vivax (Pv)- and P. falciparum (Pf)-infected patients, and 21 healthy individuals as a control group, from the Baixo Amazonas population in Pará, Brazil. The Asp299Gly polymorphisms in the Toll-like receptor 4 (TLR4), and Gly42Asp, Arg89Cys, Ala100Thr, and T-33C in the Duffy gene (FY) were analyzed by restriction fragment length polymorphism-polymerase chain reaction. The Lys1590Glu and Arg1601Gly polymorphisms in the complement receptor type 1 (CR1) were analyzed by DNA sequencing. According to the results obtained and statistical analysis considering a significance level or alpha = 0.01, we conclude that the low heterozygote frequency (2.27%) for the Asp299Gly mutation, detected in the TLR4 gene, is not related to the Pv and Pf infections in the patients analyzed. Also, the promoter region GATA-1 analysis of the FY gene in the Pv-infected patients showed that the heterozygote frequency for the T-33C mutation (11.36% of the infected patients and 20.45% of the control patients) is not related to infection resistance. Regarding the CR1 gene, the observed heterozygote frequency (9.09%) for the Arg1601Gly mutation in Pf-infected patients when compared to heterozygote frequency in the control group (18.18%) suggests that there is no correlation with infection resistance.
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Affiliation(s)
- S C Soares
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, SP, Brasil.
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Soares SC, Fratelli N, Prefumo F, Bhide A, Thilaganathan B. First-trimester uterine artery Doppler and spontaneous preterm delivery. Ultrasound Obstet Gynecol 2007; 29:146-9. [PMID: 17219368 DOI: 10.1002/uog.3919] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
OBJECTIVES To assess the relationship between first-trimester uterine artery Doppler measurements and spontaneous preterm delivery. METHODS This was a retrospective analysis of uterine artery Doppler findings at 11-14 weeks in 73 singleton pregnancies with spontaneous preterm labor and 2417 pregnancies delivered at term. RESULTS The uterine artery mean resistance index (RI) was 0.68 (coefficient of variation 19%) and 0.69 (17%) in the preterm and term delivery groups, respectively (P = 0.35). The mean pulsatility index (PI) was 1.42 (39%) and 1.42 (46%) in the term and preterm delivery groups, respectively (P = 0.95). Bilateral diastolic notches were present in 34% of preterm deliveries and 33% of controls (P = 0.84). Restricting the analysis to the 19 pregnancies with preterm delivery before 34 weeks of gestation, no significant difference from controls was observed for RI (mean 0.71, coefficient of variation 11%, P = 0.41), PI (mean 1.56, coefficient of variation 29%, P = 0.27) or the number of bilateral notches (42%, P = 0.41). CONCLUSIONS Despite pathological evidence suggesting that defective placentation is associated with spontaneous preterm delivery, first trimester uterine artery resistance, as assessed by Doppler ultrasound investigation, is not different in pregnancies subsequently complicated by preterm labor compared to pregnancies delivered at term. This finding may be explained by a late failure of trophoblast development in cases destined to deliver preterm.
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Affiliation(s)
- S C Soares
- Fetal Medicine Unit, Academic Department of Obstetrics and Gynaecology, St George's Hospital Medical School, London, UK
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Prefumo F, Fratelli N, Soares SC, Thilaganathan B. Uterine artery Doppler velocimetry at 11-14 weeks in singleton pregnancies conceived by assisted reproductive technology. Ultrasound Obstet Gynecol 2007; 29:141-5. [PMID: 17072900 DOI: 10.1002/uog.3842] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
OBJECTIVE Singleton pregnancies resulting from assisted reproductive technologies (ART) have an increased risk of preterm delivery, pre-eclampsia and intrauterine growth restriction. The aim of the present study was to determine whether first-trimester trophoblastic invasion, as assessed by uterine artery Doppler velocimetry, is different in singleton pregnancies resulting from ART compared to those conceived naturally. METHODS Case-control study on 31 singleton ART pregnancies (26 in-vitro fertilization-embryo transfer, five intracytoplasmic sperm injection) and 62 matched pregnancies conceived spontaneously. Doppler velocimetry was performed at 11-14 weeks of gestation. RESULTS The mean resistance index (coefficient of variation) was 0.70 (17%) and 0.70 (18%) in ART and controls, respectively (P = 0.92). The corresponding values for mean pulsatility index were 1.40 (44%) and 1.47 (44%) in ART and controls, respectively (P = 0.58). Pregnancies with no, unilateral or bilateral diastolic notches were 48%, 26%, 26% and 36%, 37%, 27%, in ART and controls, respectively (P = 0.43). CONCLUSION There are no differences in uterine artery Doppler indices between pregnancies obtained by invasive ART and naturally conceived matched controls. This finding suggests that there is no major difference in trophoblastic invasion of the maternal spiral arteries between ART and spontaneous pregnancies.
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Affiliation(s)
- F Prefumo
- Fetal Medicine Unit, Department of Clinical Developmental Sciences, St. George's, University of London, London, UK.
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Waitzberg DL, Bellinati-Pires R, Yamaguchi N, Massili-Oku S, Salgado MM, Hypolito IP, Soares SC, Goncalves EL, Furst P. Influence of medium-chain triglyceride-based lipid emulsion on rat polymorphonuclear cell functions. Nutrition 1996; 12:93-9. [PMID: 8724379 DOI: 10.1016/0899-9007(96)90706-6] [Citation(s) in RCA: 26] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Intravenous lipid emulsions are used as energy and essential fatty acids sources. There are controversial reports postulating in vitro and in vivo inhibitory effects of long-chain triglycerides (LCT) upon the blood polymorphonuclear leukocytes (PMNL) functions. In the present study the in vivo and in vitro effects of LCT and a physical mixture of medium- and long-chain triglycerides (MCT/LCT) emulsions were investigated on select PMNL functions, i.e., chemotaxis, phagocytosis, and bacterial killing. Blood from 20 rats was incubated with LCT, MCT, MCT/LCT, and saline, respectively. MCT-containing emulsions exhibited an inhibitory effect on all PMNL functions investigated, whereas LCT exerted an effect on the phagocytic index only. The administration of a parenteral supply of LCT, MCT/LCT, and saline for 30 h followed by saline infusion for 14 h in discontinuous mode did not influence any of the investigated PMNL functions. Similarly, continuous infusion over 44 h at increasing infusion rates up to 1.5 mL/h did not affect the PMNL functions. The obvious difference between in vitro and in vivo response of the PMNL model emphasizes the necessity for continuous monitoring of in vivo conditions. Appropriate interpretation of the data requires continuous circumspection and consideration of trials in a clinical setting.
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Affiliation(s)
- D L Waitzberg
- Department of Surgery, University of Sao Paulo Medical School, Brazil
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