51
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Martins ER, Estofolete CF, Zequini AB, Cerdeira L, de Oliveira Garcia D, Bueno MFC, Francisco GR, de Andrade LN, da Costa Darini AL, Tolentino FM, Casella T, Lincopan N, Nogueira MCL. Transfer of KPC-2 carbapenemase from Klebsiella pneumoniae to Enterobacter cloacae in a patient receiving meropenem therapy. Diagn Microbiol Infect Dis 2017; 88:287-289. [DOI: 10.1016/j.diagmicrobio.2017.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 12/31/2022]
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52
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Bueno MFC, Francisco GR, Cerdeira L, Ienne S, Souza TA, Lincopan N, de Oliveira Garcia D. Draft genome sequence of an aminoglycoside-resistant RmtG-producing Pseudomonas aeruginosa ST235 isolated from a cystic fibrosis patient. J Glob Antimicrob Resist 2017; 8:106-107. [DOI: 10.1016/j.jgar.2016.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 11/29/2022] Open
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Cerdeira L, Fernandes MR, Ienne S, Souza TA, de O Garcia D, Lincopan N. Draft genome sequence of an environmental multidrug-resistant Klebsiella pneumoniae ST340/CC258 harbouring bla CTX-M-15 and bla KPC-2 genes. J Glob Antimicrob Resist 2017; 8:108-109. [PMID: 28082142 DOI: 10.1016/j.jgar.2016.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 09/21/2016] [Revised: 11/27/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022] Open
Abstract
Anthropogenic activities, including the release of wastewater and sewage from hospitals, have contributed to the contamination of aquatic environments, raising a concern to public health. In this study, we present the first draft genome sequence of a Klebsiella pneumoniae strain (Kp171, TIET-4200) belonging to the high-risk hospital-associated clonal lineage ST340/CC258, which was recovered from a water sample collected in an urban river in Brazil.
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Affiliation(s)
- Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil.
| | - Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
| | - Susan Ienne
- Core Facility for Scientific Research, University of Sao Paulo (CEFAP-USP/GENIAL), São Paulo, Brazil
| | - Tiago A Souza
- Core Facility for Scientific Research, University of Sao Paulo (CEFAP-USP/GENIAL), São Paulo, Brazil
| | | | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.
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54
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Moura Q, Fernandes MR, Cerdeira L, Ienne S, Souza TA, Negrão FJ, Lincopan N. Draft genome sequence of a multidrug-resistant CMY-2-producing Salmonella enterica subsp. enterica serovar Minnesota ST3088 isolated from chicken meat. J Glob Antimicrob Resist 2016; 8:67-69. [PMID: 28017672 DOI: 10.1016/j.jgar.2016.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/20/2016] [Accepted: 10/31/2016] [Indexed: 11/19/2022] Open
Affiliation(s)
- Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Susan Ienne
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tiago A Souza
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fábio Juliano Negrão
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados, Mato Grosso do Sul, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
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da Silva KC, Cunha MPV, Cerdeira L, de Oliveira MGX, de Oliveira MCV, Gomes CR, Lincopan N, Knöbl T, Moreno AM. High-virulence CMY-2- and CTX-M-2-producing avian pathogenic Escherichia coli strains isolated from commercial turkeys. Diagn Microbiol Infect Dis 2016; 87:64-67. [PMID: 27773543 DOI: 10.1016/j.diagmicrobio.2016.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 07/18/2016] [Revised: 09/21/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022]
Abstract
This study reports the high-virulence phylogenetic backgrounds of CMY-2- and CTX-M-2-producing avian pathogenic Escherichia coli strains isolated from turkeys sent to slaughter and condemned by airsacculitis in Brazil. Among 300 air sac samples, seven E. coli strains produced plasmid-mediated CMY-2-type AmpC, of which three carried also the blaCTX-M-2 Extended Spectrum Beta-Lactamase encoding gene. Interestingly, the transfer of the blaCMY-2 gene was positive for three E. coli strains, being associated with the presence of IncI1 plasmids. The complete sequence of the representative pJB10 plasmid revealed that the blaCMY-2 gene was within a transposon-like element in the classical genetic environment consisting of tnpA-blaCMY-2-blc-sugE structure. This plasmid with 94-kb belonged to the sequence type (ST) 12 among IncI1 plasmids, which has been associated with the worldwide spread of blaCMY-2 among Salmonella enterica and E. coli. Furthermore, to the best of our knowledge, this is the first complete sequence of a CMY-2-encoding plasmid derived from an Escherichia coli isolated from food-producing animals in Latin America.
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Affiliation(s)
- Ketrin Cristina da Silva
- Department of Preventive Veterinary Medicine and Animal Health, University of São Paulo, College of Veterinary Medicine and Zootechny, São Paulo, Brazil
| | - Marcos Paulo Vieira Cunha
- Department of Pathology, University of São Paulo, College of Veterinary Medicine and Zootechnics, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | | | | | - Cleise Ribeiro Gomes
- Department of Preventive Veterinary Medicine and Animal Health, University of São Paulo, College of Veterinary Medicine and Zootechny, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Terezinha Knöbl
- Department of Pathology, University of São Paulo, College of Veterinary Medicine and Zootechnics, São Paulo, Brazil
| | - Andrea Micke Moreno
- Department of Preventive Veterinary Medicine and Animal Health, University of São Paulo, College of Veterinary Medicine and Zootechny, São Paulo, Brazil.
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Marinotti O, Cerqueira GC, de Almeida LGP, Ferro MIT, Loreto ELDS, Zaha A, Teixeira SMR, Wespiser AR, Almeida E Silva A, Schlindwein AD, Pacheco ACL, Silva ALDCD, Graveley BR, Walenz BP, Lima BDA, Ribeiro CAG, Nunes-Silva CG, de Carvalho CR, Soares CMDA, de Menezes CBA, Matiolli C, Caffrey D, Araújo DAM, de Oliveira DM, Golenbock D, Grisard EC, Fantinatti-Garboggini F, de Carvalho FM, Barcellos FG, Prosdocimi F, May G, Azevedo Junior GMD, Guimarães GM, Goldman GH, Padilha IQM, Batista JDS, Ferro JA, Ribeiro JMC, Fietto JLR, Dabbas KM, Cerdeira L, Agnez-Lima LF, Brocchi M, de Carvalho MO, Teixeira MDM, Diniz Maia MDM, Goldman MHS, Cruz Schneider MP, Felipe MSS, Hungria M, Nicolás MF, Pereira M, Montes MA, Cantão ME, Vincentz M, Rafael MS, Silverman N, Stoco PH, Souza RC, Vicentini R, Gazzinelli RT, Neves RDO, Silva R, Astolfi-Filho S, Maciel TEF, Urményi TP, Tadei WP, Camargo EP, de Vasconcelos ATR. The genome of Anopheles darlingi, the main neotropical malaria vector. Nucleic Acids Res 2013; 41:7387-400. [PMID: 23761445 PMCID: PMC3753621 DOI: 10.1093/nar/gkt484] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [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] [Indexed: 02/03/2023] Open
Abstract
Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ∼100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae. More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vector–human and vector–parasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible at www.labinfo.lncc.br/index.php/anopheles-darlingi.
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Affiliation(s)
- Osvaldo Marinotti
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA, Institute of Technology, Broad Institute of Harvard and Massachusetts, Cambridge, MA 02141, USA, Laboratório de Bioinformática do Laboratório Nacional de Computação Científica, Petrópolis, RJ 25651-075, Brasil, Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP -Universidade Estadual Paulista, SP 14884-900, Brasil, Departamento de Biologia, Universidade Federal de Santa Maria, Santa Maria, RS 97105-900, Brasil, Departamento de Biologia Molecular e Biotecnologia, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brasil, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270901, Brasil, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA, Laboratório de Entomologia Médica IPEPATRO/FIOCRUZ, Porto Velho, RO 76812-245, Brasil, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brasil, Centro de Ciências da Saúde, Universidade Estadual do Ceará, Fortaleza, CE 62042-280, Brasil, Departamento de Ciências Biológicas, Campus Senador Helvídio Nunes de Barros, Universidade Federal do Piauí, Picos, PI 60740-000, Brasil, Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA 66075-900, Brasil, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030, USA, Informatics, The J. Craig Venter Institute, Medical Center Drive, Rockville, MD 20850, USA, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-862, Brasil, Departamento de Genética e Melhoramento, Universidade Federal de Viçosa, MG 36570-000, Brasil, Centro de Apoio Mul
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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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