1
|
Côrtes MF, Botelho AMN, Bandeira PT, Mouton W, Badiou C, Bes M, Lima NCB, Soares AER, Souza RC, Almeida LGP, Martins-Simoes P, Vasconcelos ATR, Nicolás MF, Laurent F, Planet PJ, Figueiredo AMS. Reductive evolution of virulence repertoire to drive the divergence between community- and hospital-associated methicillin-resistant Staphylococcus aureus of the ST1 lineage. Virulence 2021; 12:951-967. [PMID: 33734031 PMCID: PMC7993186 DOI: 10.1080/21505594.2021.1899616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 01/26/2021] [Accepted: 03/01/2021] [Indexed: 01/01/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) of the ST1-SCCmecIV lineage has been associated with community-acquired (CA) infections in North America and Australia. In Brazil, multi-drug resistant ST1-SCCmecIV MRSA has emerged in hospital-associated (HA) diseases in Rio de Janeiro. To understand these epidemiological differences, genomic and phylogenetic analyses were performed. In addition, virulence assays were done for representative CA - and HA-MRSA strains. Despite the conservation of the virulence repertoire, some genes were missing in Brazilian ST1-SCCmecIV including lukSF-PV, fnbB, and several superantigen-encoded genes. Additionally, CA-MRSA lost the splDE while HA-MRSA strains conserved the complete operon. Most of these variable genes were located in mobile genetic elements (MGE). However, conservation and maintenance of MGEs were often observed despite the absence of their associated virulence markers. A Bayesian phylogenetic tree revealed the occurrence of more than one entrance of ST1 strains in Rio de Janeiro. The tree shape and chronology allowed us to infer that the hospital-associated ST1-SCCmecIV from Brazil and the community-acquired USA400 from North America are not closely related and that they might have originated from different MSSA strains that independently acquired SCCmecIV cassettes. As expected, representatives of ST1 strains from Brazil showed lower cytotoxicity and a greater ability to survive inside human host cells. We suggest that Brazilian ST1-SCCmecIV strains have adapted to the hospital setting by reducing virulence and gaining the ability to persist and survive inside host cells. Possibly, these evolutionary strategies may balance the biologic cost of retaining multiple antibiotic resistance genes.
Collapse
Affiliation(s)
- Marina Farrel Côrtes
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Faculté de Médecine Lyon Est, Université de Lyon, Domaine de la Buire, Lyon, France
| | - Ana Maria N. Botelho
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paula Terra Bandeira
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - William Mouton
- Centre International de Recherche en Infectiologie (CIRI)―team Pathogénie des Staphylococques―Université Lyon 1, École Normale Supérieure de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils De Lyon, Lyon, France
| | - Cedric Badiou
- Centre International de Recherche en Infectiologie (CIRI)―team Pathogénie des Staphylococques―Université Lyon 1, École Normale Supérieure de Lyon, Lyon, France
| | - Michèle Bes
- Centre International de Recherche en Infectiologie (CIRI)―team Pathogénie des Staphylococques―Université Lyon 1, École Normale Supérieure de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils De Lyon, Lyon, France
- Laboratoire de Bactériologie, Centre de Biologie et de Pathologie Nord, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Nicholas C. B. Lima
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | | | - Rangel C. Souza
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Luiz G. P. Almeida
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Patricia Martins-Simoes
- Centre International de Recherche en Infectiologie (CIRI)―team Pathogénie des Staphylococques―Université Lyon 1, École Normale Supérieure de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils De Lyon, Lyon, France
- Laboratoire de Bactériologie, Centre de Biologie et de Pathologie Nord, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | | | - Marisa F. Nicolás
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Frédéric Laurent
- Faculté de Médecine Lyon Est, Université de Lyon, Domaine de la Buire, Lyon, France
- Centre International de Recherche en Infectiologie (CIRI)―team Pathogénie des Staphylococques―Université Lyon 1, École Normale Supérieure de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils De Lyon, Lyon, France
- Laboratoire de Bactériologie, Centre de Biologie et de Pathologie Nord, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Paul J. Planet
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Agnes M. S. Figueiredo
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
2
|
Penna B, Silva MB, Soares AER, Vasconcelos ATR, Ramundo MS, Ferreira FA, Silva-Carvalho MC, de Sousa VS, Rabello RF, Bandeira PT, de Souza VS, Planet PJ, Vieira-da-Motta O, Botelho AMN, Figueiredo AMS. Comparative genomics of MRSA strains from human and canine origins reveals similar virulence gene repertoire. Sci Rep 2021; 11:4724. [PMID: 33633263 PMCID: PMC7907190 DOI: 10.1038/s41598-021-83993-5] [Citation(s) in RCA: 7] [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: 08/19/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen associated with a wide variety of infections in humans. The ability of MRSA to infect companion animals has gained increasing attention in the scientific literature. In this study, 334 dogs were screened for MRSA in two cities located in Rio de Janeiro State. The prevalence of MRSA in dogs was 2.7%. Genotyping revealed isolates from sequence types (ST) 1, 5, 30, and 239 either colonizing or infecting dogs. The genome of the canine ST5 MRSA (strain SA112) was compared with ST5 MRSA from humans-the main lineage found in Rio de Janeiro hospitals-to gain insights in the origin of this dog isolate. Phylogenetic analysis situated the canine genome and human strain CR14-035 in the same clade. Comparative genomics revealed similar virulence profiles for SA112 and CR14-035. Both genomes carry S. aureus genomic islands νSAα, νSAβ, and νSAγ. The virulence potential of the canine and human strains was similar in a Caenorhabditis elegans model. Together, these results suggest a potential of canine MRSA to infect humans and vice versa. The circulation in community settings of a MRSA lineage commonly found in hospitals is an additional challenge for public health surveillance authorities.
Collapse
Affiliation(s)
- Bruno Penna
- grid.411173.10000 0001 2184 6919Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Marcella B. Silva
- grid.412331.60000 0000 9087 6639Laboratório de Sanidade Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - André E. R. Soares
- grid.452576.70000 0004 0602 9007Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Ana T. R. Vasconcelos
- grid.452576.70000 0004 0602 9007Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Mariana S. Ramundo
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabienne A. Ferreira
- grid.411237.20000 0001 2188 7235Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina Brazil
| | - Maria C. Silva-Carvalho
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viviane S. de Sousa
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata F. Rabello
- grid.411173.10000 0001 2184 6919Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Paula T. Bandeira
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil ,grid.8536.80000 0001 2294 473XInstituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viviane S. de Souza
- grid.8536.80000 0001 2294 473XInstituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paul J. Planet
- grid.25879.310000 0004 1936 8972Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Olney Vieira-da-Motta
- grid.412331.60000 0000 9087 6639Laboratório de Sanidade Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Ana M. N. Botelho
- grid.411173.10000 0001 2184 6919Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil ,grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Agnes M. S. Figueiredo
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
3
|
Aguiar RS, Pohl F, Morais GL, Nogueira FCS, Carvalho JB, Guida L, Arge LWP, Melo A, Moreira MEL, Cunha DP, Gomes L, Portari EA, Velasquez E, Melani RD, Pezzuto P, de Castro FL, Geddes VEV, Gerber AL, Azevedo GS, Schamber-Reis BL, Gonçalves AL, Junqueira-de-Azevedo I, Nishiyama MY, Ho PL, Schanoski AS, Schuch V, Tanuri A, Chimelli L, Vasconcelos ZFM, Domont GB, Vasconcelos ATR, Nakaya HI. Molecular alterations in the extracellular matrix in the brains of newborns with congenital Zika syndrome. Sci Signal 2020; 13:eaay6736. [PMID: 32518143 DOI: 10.1126/scisignal.aay6736] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Zika virus (ZIKV) infection during pregnancy can cause a set of severe abnormalities in the fetus known as congenital Zika syndrome (CZS). Experiments with animal models and in vitro systems have substantially contributed to our understanding of the pathophysiology of ZIKV infection. Here, to investigate the molecular basis of CZS in humans, we used a systems biology approach to integrate transcriptomic, proteomic, and genomic data from the postmortem brains of neonates with CZS. We observed that collagens were greatly reduced in expression in CZS brains at both the RNA and protein levels and that neonates with CZS had several single-nucleotide polymorphisms in collagen-encoding genes that are associated with osteogenesis imperfecta and arthrogryposis. These findings were validated by immunohistochemistry and comparative analysis of collagen abundance in ZIKV-infected and uninfected samples. In addition, we showed a ZIKV-dependent increase in the expression of cell adhesion factors that are essential for neurite outgrowth and axon guidance, findings that are consistent with the neuronal migration defects observed in CZS. Together, these findings provide insights into the underlying molecular alterations in the ZIKV-infected brain and reveal host genes associated with CZS susceptibility.
Collapse
Affiliation(s)
- Renato S Aguiar
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fabio Pohl
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Guilherme L Morais
- National Laboratory of Scientific Computation, LNCC/MCTI, Petrópolis, Brazil
| | - Fabio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joseane B Carvalho
- National Laboratory of Scientific Computation, LNCC/MCTI, Petrópolis, Brazil
| | - Letícia Guida
- Fernandes Figueira Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Luis W P Arge
- National Laboratory of Scientific Computation, LNCC/MCTI, Petrópolis, Brazil
| | - Adriana Melo
- Instituto de Pesquisa Professor Amorim Neto, Campina Grande, Paraíba, Brazil
| | | | - Daniela P Cunha
- Fernandes Figueira Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Leonardo Gomes
- Fernandes Figueira Institute, Fiocruz, Rio de Janeiro, Brazil
| | | | - Erika Velasquez
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael D Melani
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paula Pezzuto
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda L de Castro
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victor E V Geddes
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandra L Gerber
- National Laboratory of Scientific Computation, LNCC/MCTI, Petrópolis, Brazil
| | - Girlene S Azevedo
- Instituto de Pesquisa Professor Amorim Neto, Campina Grande, Paraíba, Brazil
| | - Bruno L Schamber-Reis
- Faculdade de Ciências Médicas de Campina Grande, Núcleo de Genética Médica, Centro Universitário UniFacisa, Campina Grande, Paraíba, Brazil
| | - Alessandro L Gonçalves
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Milton Y Nishiyama
- Special Laboratory for Applied Toxinology, Butantan Institute, São Paulo, Brazil
| | - Paulo L Ho
- Bacteriology Laboratory, Butantan Institute, São Paulo, Brazil
| | | | - Viviane Schuch
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Amilcar Tanuri
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leila Chimelli
- Laboratório de Neuropatologia, Instituto Estadual do Cérebro, Rio de Janeiro, Brazil.
| | | | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Ana T R Vasconcelos
- National Laboratory of Scientific Computation, LNCC/MCTI, Petrópolis, Brazil.
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
- Scientific Platform Pasteur-USP, São Paulo, Brazil
| |
Collapse
|
4
|
Nascimento APB, Ortiz MF, Martins WMBS, Morais GL, Fehlberg LCC, Almeida LGP, Ciapina LP, Gales AC, Vasconcelos ATR. Intraclonal Genome Stability of the Metallo-β-lactamase SPM-1-producing Pseudomonas aeruginosa ST277, an Endemic Clone Disseminated in Brazilian Hospitals. Front Microbiol 2016; 7:1946. [PMID: 27994579 PMCID: PMC5136561 DOI: 10.3389/fmicb.2016.01946] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 09/23/2016] [Accepted: 11/21/2016] [Indexed: 01/30/2023] Open
Abstract
Carbapenems represent the mainstay therapy for the treatment of serious P. aeruginosa infections. However, the emergence of carbapenem resistance has jeopardized the clinical use of this important class of compounds. The production of SPM-1 metallo-β-lactamase has been the most common mechanism of carbapenem resistance identified in P. aeruginosa isolated from Brazilian medical centers. Interestingly, a single SPM-1-producing P. aeruginosa clone belonging to the ST277 has been widely spread within the Brazilian territory. In the current study, we performed a next-generation sequencing of six SPM-1-producing P. aeruginosa ST277 isolates. The core genome contains 5899 coding genes relative to the reference strain P. aeruginosa PAO1. A total of 26 genomic islands were detected in these isolates. We identified remarkable elements inside these genomic islands, such as copies of the blaSPM−1 gene conferring resistance to carbapenems and a type I-C CRISPR-Cas system, which is involved in protection of the chromosome against foreign DNA. In addition, we identified single nucleotide polymorphisms causing amino acid changes in antimicrobial resistance and virulence-related genes. Together, these factors could contribute to the marked resistance and persistence of the SPM-1-producing P. aeruginosa ST277 clone. A comparison of the SPM-1-producing P. aeruginosa ST277 genomes showed that their core genome has a high level nucleotide similarity and synteny conservation. The variability observed was mainly due to acquisition of genomic islands carrying several antibiotic resistance genes.
Collapse
Affiliation(s)
- Ana P B Nascimento
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Mauro F Ortiz
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Willames M B S Martins
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Guilherme L Morais
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Lorena C C Fehlberg
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Luiz G P Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Luciane P Ciapina
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Ana C Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Ana T R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| |
Collapse
|
5
|
Botelho AMN, Costa MOC, Beltrame CO, Ferreira FA, Lima NCB, Costa BSS, de Morais GL, Souza RC, Almeida LGP, Vasconcelos ATR, Nicolás MF, Figueiredo AMS. Complete Genome Sequence of the MRSA Isolate HC1335 from ST239 Lineage Displaying a Truncated AgrC Histidine Kinase Receptor. Genome Biol Evol 2016; 8:3187-3192. [PMID: 27635055 PMCID: PMC5174738 DOI: 10.1093/gbe/evw225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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] [Indexed: 01/30/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is still one of the most important hospital pathogen globally. The multiresistant isolates of the ST239-SCCmecIII lineage are spread over large geographic regions, colonizing and infecting hospital patients in virtually all continents. The balance between fitness (adaptability) and virulence potential is likely to represent an important issue in the clonal shift dynamics leading the success of some specific MRSA clones over another. The accessory gene regulator (agr) is the master quorum sensing system of staphylococci playing a role in the global regulation of key virulence factors. Consequently, agr inactivation in S. aureus may represent a significant mechanism of genetic variability in the adaptation of this healthcare-associated pathogen. We report here the complete genome sequence of the methicillin-resistant S. aureus, isolate HC1335, a variant of the ST239 lineage, which presents a natural insertion of an IS256 transposase element in the agrC gene encoding AgrC histidine kinase receptor.
Collapse
Affiliation(s)
- Ana M N Botelho
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maiana O C Costa
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Cristiana O Beltrame
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabienne A Ferreira
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Bruno S S Costa
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Rangel C Souza
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Luiz G P Almeida
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | | | - Marisa F Nicolás
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Agnes M S Figueiredo
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
6
|
Ferrarini MG, Siqueira FM, Mucha SG, Palama TL, Jobard É, Elena-Herrmann B, R Vasconcelos AT, Tardy F, Schrank IS, Zaha A, Sagot MF. Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling. BMC Genomics 2016; 17:353. [PMID: 27178561 PMCID: PMC4866288 DOI: 10.1186/s12864-016-2644-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 02/09/2016] [Accepted: 04/22/2016] [Indexed: 12/24/2022] Open
Abstract
Background The respiratory tract of swine is colonized by several bacteria among which are three Mycoplasma species: Mycoplasma flocculare, Mycoplasma hyopneumoniae and Mycoplasma hyorhinis. While colonization by M. flocculare is virtually asymptomatic, M. hyopneumoniae is the causative agent of enzootic pneumonia and M. hyorhinis is present in cases of pneumonia, polyserositis and arthritis. The genomic resemblance among these three Mycoplasma species combined with their different levels of pathogenicity is an indication that they have unknown mechanisms of virulence and differential expression, as for most mycoplasmas. Methods In this work, we performed whole-genome metabolic network reconstructions for these three mycoplasmas. Cultivation tests and metabolomic experiments through nuclear magnetic resonance spectroscopy (NMR) were also performed to acquire experimental data and further refine the models reconstructed in silico. Results Even though the refined models have similar metabolic capabilities, interesting differences include a wider range of carbohydrate uptake in M. hyorhinis, which in turn may also explain why this species is a widely contaminant in cell cultures. In addition, the myo-inositol catabolism is exclusive to M. hyopneumoniae and may be an important trait for virulence. However, the most important difference seems to be related to glycerol conversion to dihydroxyacetone-phosphate, which produces toxic hydrogen peroxide. This activity, missing only in M. flocculare, may be directly involved in cytotoxicity, as already described for two lung pathogenic mycoplasmas, namely Mycoplasma pneumoniae in human and Mycoplasma mycoides subsp. mycoides in ruminants. Metabolomic data suggest that even though these mycoplasmas are extremely similar in terms of genome and metabolism, distinct products and reaction rates may be the result of differential expression throughout the species. Conclusions We were able to infer from the reconstructed networks that the lack of pathogenicity of M. flocculare if compared to the highly pathogenic M. hyopneumoniae may be related to its incapacity to produce cytotoxic hydrogen peroxide. Moreover, the ability of M. hyorhinis to grow in diverse sites and even in different hosts may be a reflection of its enhanced and wider carbohydrate uptake. Altogether, the metabolic differences highlighted in silico and in vitro provide important insights to the different levels of pathogenicity observed in each of the studied species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2644-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mariana G Ferrarini
- ERABLE, Inria, 43, Bd du 11 Novembre 1918, Villeurbanne, France.,CBiot, UFRGS, Av Bento Gon'calves, Porto Alegre, 9500, Brazil.,Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, 43, Bd du 11 Novembre 1918, Villeurbanne, France
| | | | - Scheila G Mucha
- CBiot, UFRGS, Av Bento Gon'calves, Porto Alegre, 9500, Brazil
| | - Tony L Palama
- Université de Lyon, Institut des Sciences Analytiques (CNRS, ENS Lyon, Université Lyon 1), 5, Rue de la Doua, Villeurbanne, France.,Current address: LISBP - INSA Toulouse, Toulouse, France
| | - Élodie Jobard
- Université de Lyon, Institut des Sciences Analytiques (CNRS, ENS Lyon, Université Lyon 1), 5, Rue de la Doua, Villeurbanne, France
| | - Bénédicte Elena-Herrmann
- Université de Lyon, Institut des Sciences Analytiques (CNRS, ENS Lyon, Université Lyon 1), 5, Rue de la Doua, Villeurbanne, France.,Université de Lyon, Centre Léon Bérard, Département d'oncologie médicale, 28, rue Laënnec, Lyon, France
| | - Ana T R Vasconcelos
- Laboratório Nacional de Computaćão Científica, Av. Getúlio Vargas, 333, Petrópolis, Brazil
| | - Florence Tardy
- Anses, Laboratoire de Lyon, UMR Mycoplasmoses des Ruminants, 31, Av Tony Garnier, Lyon, France.,Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, 1 Avenue Bourgelat, Marcy L'Étoile, France
| | - Irene S Schrank
- CBiot, UFRGS, Av Bento Gon'calves, Porto Alegre, 9500, Brazil
| | - Arnaldo Zaha
- CBiot, UFRGS, Av Bento Gon'calves, Porto Alegre, 9500, Brazil
| | - Marie-France Sagot
- ERABLE, Inria, 43, Bd du 11 Novembre 1918, Villeurbanne, France. .,Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, 43, Bd du 11 Novembre 1918, Villeurbanne, France.
| |
Collapse
|
7
|
Botelho AMN, Costa MOC, Beltrame CO, Ferreira FA, Côrtes MF, Bandeira PT, Lima NCB, Souza RC, Almeida LGP, Vasconcelos ATR, Nicolás MF, Figueiredo AMS. Complete genome sequence of an agr-dysfunctional variant of the ST239 lineage of the methicillin-resistant Staphylococcus aureus strain GV69 from Brazil. Stand Genomic Sci 2016; 11:34. [PMID: 27152133 PMCID: PMC4857242 DOI: 10.1186/s40793-016-0154-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 04/25/2016] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus aureus is a versatile Gram-positive coccus frequently found colonizing the skin and nasal membranes of humans. The acquisition of the staphylococcal cassette chromosome mec was a major milestone in the evolutionary path of methicillin-resistant S. aureus. This genetic element carries the mecA gene, the main determinant of methicillin resistance. MRSA is involved in a plethora of opportunistic infectious diseases. The accessory gene regulator is the major S. aureus quorum sensing system, playing an important role in staphylococcal virulence, including the development of biofilms. We report the complete genome sequence (NCBI BioProject ID: PRJNA264181) of the methicillin-resistant S. aureus strain GV69 (= CMVRS P4521), a variant of the ST239 lineage that presents with a natural attenuation of agr-RNAIII transcription and a moderate accumulation of biofilm.
Collapse
Affiliation(s)
- Ana M N Botelho
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| | - Maiana O C Costa
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Cristiana O Beltrame
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| | - Fabienne A Ferreira
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| | - Marina F Côrtes
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| | - Paula T Bandeira
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| | - Nicholas C B Lima
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Rangel C Souza
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Luiz G P Almeida
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Ana T R Vasconcelos
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Marisa F Nicolás
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075 RJ Brazil
| | - Agnes M S Figueiredo
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902 RJ Brazil
| |
Collapse
|
8
|
Pacchioni RG, Carvalho FM, Thompson CE, Faustino ALF, Nicolini F, Pereira TS, Silva RCB, Cantão ME, Gerber A, Vasconcelos ATR, Agnez-Lima LF. Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil. Microbiologyopen 2014; 3:299-315. [PMID: 24706600 PMCID: PMC4082704 DOI: 10.1002/mbo3.169] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 02/23/2014] [Accepted: 02/25/2014] [Indexed: 12/20/2022] Open
Abstract
Although microorganisms play crucial roles in ecosystems, metagenomic analyses of soil samples are quite scarce, especially in the Southern Hemisphere. In this work, the microbial diversity of soil samples from an Atlantic Forest and Caatinga was analyzed using a metagenomic approach. Proteobacteria and Actinobacteria were the dominant phyla in both samples. Among which, a significant proportion of stress-resistant bacteria associated to organic matter degradation was found. Sequences related to metabolism of amino acids, nitrogen, and DNA and stress resistance were more frequent in Caatinga soil, while the forest sample showed the highest occurrence of hits annotated in phosphorous metabolism, defense mechanisms, and aromatic compound degradation subsystems. The principal component analysis (PCA) showed that our samples are close to the desert metagenomes in relation to taxonomy, but are more similar to rhizosphere microbiota in relation to the functional profiles. The data indicate that soil characteristics affect the taxonomic and functional distribution; these characteristics include low nutrient content, high drainage (both are sandy soils), vegetation, and exposure to stress. In both samples, a rapid turnover of organic matter with low greenhouse gas emission was suggested by the functional profiles obtained, reinforcing the importance of preserving natural areas.
Collapse
Affiliation(s)
- Ralfo G Pacchioni
- Department of Cellular Biology and Genetics, UFRN, Natal, Rio Grande do Norte, Brazil
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Varani AM, Monteiro-Vitorello CB, de Almeida LGP, Souza RC, Cunha OL, Lima WC, Civerolo E, Van Sluys MA, Vasconcelos ATR. Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains. Genet Mol Biol 2012; 35:149-52. [PMID: 22481888 PMCID: PMC3313504 DOI: 10.1590/s1415-47572012005000019] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 12/09/2011] [Indexed: 11/21/2022] Open
Abstract
The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.
Collapse
Affiliation(s)
- Alessandro M Varani
- Genome and Transposable Elements Laboratory, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Sant'Anna FH, Almeida LGP, Cecagno R, Reolon LA, Siqueira FM, Machado MRS, Vasconcelos ATR, Schrank IS. Genomic insights into the versatility of the plant growth-promoting bacterium Azospirillum amazonense. BMC Genomics 2011; 12:409. [PMID: 21838888 PMCID: PMC3169532 DOI: 10.1186/1471-2164-12-409] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [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: 04/29/2011] [Accepted: 08/12/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The species Azospirillum amazonense belongs to a well-known genus of plant growth-promoting bacteria. This bacterium is found in association with several crops of economic importance; however, there is a lack of information on its physiology. In this work, we present a comprehensive analysis of the genomic features of this species. RESULTS Genes of A. amazonense related to nitrogen/carbon metabolism, energy production, phytohormone production, transport, quorum sensing, antibiotic resistance, chemotaxis/motility and bacteriophytochrome biosynthesis were identified. Noteworthy genes were the nitrogen fixation genes and the nitrilase gene, which could be directly implicated in plant growth promotion, and the carbon fixation genes, which had previously been poorly investigated in this genus. One important finding was that some A. amazonense genes, like the nitrogenase genes and RubisCO genes, were closer phylogenetically to Rhizobiales members than to species of its own order. CONCLUSION The species A. amazonense presents a versatile repertoire of genes crucial for its plant-associated lifestyle.
Collapse
Affiliation(s)
- Fernando H Sant'Anna
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av, Bento Gonçalves, 9500 Campus do Vale, Porto Alegre, RS, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Veiga DFT, Vicente FFR, Grivet M, de la Fuente A, Vasconcelos ATR. Genome-wide partial correlation analysis of Escherichia coli microarray data. Genet Mol Res 2007; 6:730-742. [PMID: 18058701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Transcriptional control is an essential regulatory mechanism employed by bacteria. Much about transcriptional regulation remains to be discovered, even for the most widely studied bacterium, Escherichia coli. In the present study, we made a genome-wide low-order partial correlation analysis of E. coli microarray data with the purpose of recovering regulatory interactions from transcriptome data. As a result, we produced whole genome transcription factor regulation and co-regulation graphs using the predicted interactions, and we demonstrated how they can be used to investigate regulation and biological function. We concluded that partial correlation analysis can be employed as a method to predict putative regulatory interactions from expression data, as a complementary approach to transcription factor binding site tools and other tools designed to detect co-regulated genes.
Collapse
Affiliation(s)
- D F T Veiga
- Laboratório Nacional de Computação Científica, Laboratório de Bioinformática, Petrópolis, RJ, Brasil.
| | | | | | | | | |
Collapse
|
12
|
Hungria M, Astolfi-Filho S, Chueire LMO, Nicolás MF, Santos EBP, Bulbol MR, Souza-Filho A, Nogueira Assunção E, Germano MG, Vasconcelos ATR. Genetic characterization of Chromobacterium isolates from black water environments in the Brazilian Amazon. Lett Appl Microbiol 2005; 41:17-23. [PMID: 15960747 DOI: 10.1111/j.1472-765x.2005.01724.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [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: 11/29/2022]
Abstract
AIMS To isolate and to characterize the diversity of Chromobacterium violaceum from the Brazilian Amazon region. METHODS AND RESULTS Twenty-two isolates were obtained from the waters and banks of the river Negro, in the Brazilian Amazon. All isolates were able to grow in vitro at 44 degrees C and pH 4.0, but were adversely affected by temperatures below 15 degrees C, and unable to survive at 4 degrees C, properties that may be related to the adaptation to the ecosystem. The isolates were joined at a final level of similarity of only 13% in the rep-PCR analysis. The analysis of 16S rRNA genes resulted in three main groups clustered at a final level of similarity of 97% and only three isolates were clustered with the type strain. Similar data were obtained for the 23S rRNA gene. CONCLUSIONS A high level of genetic diversity was verified with indications that the Brazilian isolates would fit into at least two new clusters besides C. violaceum species. SIGNIFICANCE AND IMPACT OF THE STUDY The results show remarkable bacterial adaptability and genetic diversity of C. violaceum in the Amazon region.
Collapse
|