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Michetti M, Gualtieri M, Anav A, Adani M, Benassi B, Dalmastri C, D'Elia I, Piersanti A, Sannino G, Zanini G, Uccelli R. Climate change and air pollution: Translating their interplay into present and future mortality risk for Rome and Milan municipalities. Sci Total Environ 2022; 830:154680. [PMID: 35314224 DOI: 10.1016/j.scitotenv.2022.154680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Heat and cold temperatures associated with exposure to poor air quality lead to increased mortality. Using a generalized linear model with Poisson regression for overdispersion, this study quantifies the natural-caused mortality burden attributable to heat/cold temperatures and PM10 and O3 air pollutants in Rome and Milan, the two most populated Italian cities. We calculate local-specific mortality relative risks (RRs) for the period 2004-2015 considering the overall population and the most vulnerable age category (≥85 years). Combining a regional climate model with a chemistry-transport model under future climate and air pollution scenarios (RCP2.6 and RCP8.5), we then project mortality to 2050. Results show that for historical mortality the burden is much larger for cold than for warm temperatures. RR peaks during wintertime in Milan and summertime in Rome, highlighting the relevance of accounting for the effects of air pollution besides that of climate, in particular PM10 for Milan and O3 for Rome. Overall, Milan reports higher RRs while, in both cities, the elderly appear more susceptible to heat/cold and air pollution events than the average population. Two counterbalancing effects shape mortality in the future: an increase associated with higher and more frequent warmer daily temperatures - especially in the case of climate inaction - and a decrease due to declining cold-mortality burden. The outcomes highlight the urgent need to adopt more stringent and integrated climate and air quality policies to reduce the temperature and air pollution combined effects on health.
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Affiliation(s)
- M Michetti
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Bologna, Via Martiri di Monte Sole 4, 40129 Bologna, Italy.
| | - M Gualtieri
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Bologna, Via Martiri di Monte Sole 4, 40129 Bologna, Italy
| | - A Anav
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Roma Casaccia, Via Anguillarese 301, 00123 Santa Maria di Galeria, Rome, Italy
| | - M Adani
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Bologna, Via Martiri di Monte Sole 4, 40129 Bologna, Italy
| | - B Benassi
- Division of Health Protection Technologies, ENEA Centro Ricerche Roma Casaccia, Via Anguillarese 301, 00123 Santa Maria di Galeria, Rome, Italy
| | - C Dalmastri
- Division of Health Protection Technologies, ENEA Centro Ricerche Roma Casaccia, Via Anguillarese 301, 00123 Santa Maria di Galeria, Rome, Italy
| | - I D'Elia
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Roma, Lungotevere Thaon de Revel, 76, 00196 Rome, Italy
| | - A Piersanti
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Bologna, Via Martiri di Monte Sole 4, 40129 Bologna, Italy
| | - G Sannino
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Roma Casaccia, Via Anguillarese 301, 00123 Santa Maria di Galeria, Rome, Italy
| | - G Zanini
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Bologna, Via Martiri di Monte Sole 4, 40129 Bologna, Italy
| | - R Uccelli
- Division of Health Protection Technologies, ENEA Centro Ricerche Roma Casaccia, Via Anguillarese 301, 00123 Santa Maria di Galeria, Rome, Italy
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Michetti M, Adani M, Anav A, Benassi B, Dalmastri C, D'Elia I, Gualtieri M, Piersanti A, Sannino G, Uccelli R, Zanini G. From single to multivariable exposure models to translate climatic and air pollution effects into mortality risk. A customized application to the city of Rome, Italy. MethodsX 2022; 9:101717. [PMID: 35620759 PMCID: PMC9127213 DOI: 10.1016/j.mex.2022.101717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/06/2021] [Accepted: 04/22/2022] [Indexed: 11/29/2022] Open
Abstract
This study presents an approach developed to derive a Delayed-Multivariate Exposure-Response Model (D-MERF) useful to assess the short-term influence of temperature on mortality, accounting also for the effect of air pollution (O3 and PM10). By using Distributed, lag non-linear models (DLNM) we explain how city-specific exposure-response functions are derived for the municipality of Rome, which is taken as an example. The steps illustrated can be replicated to other cities while the statistical model presented here can be further extended to other exposure variables. We derive the mortality relative-risk (RR) curve averaged over the period 2004–2015, which accounts for city-specific climate and pollution conditions. Key aspects of customization are as follows: This study reports the steps followed to derive a combined, multivariate exposure-response model aimed at translating climatic and air pollution effects into mortality risk. Integration of climate and air pollution parameters to derive RR values. A specific interest is devoted to the investigation of delayed effects on mortality in the presence of different exposure factors.
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Affiliation(s)
- M. Michetti
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Bologna, Via Martiri di Monte Sole 4, Bologna 40129, Italy
- Corresponding author.
| | - M. Adani
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Bologna, Via Martiri di Monte Sole 4, Bologna 40129, Italy
| | - A. Anav
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Roma Casaccia, Via Anguillarese 301, Rome, Santa Maria di Galeria 00123, Italy
| | - B. Benassi
- Division of Health Protection Technologies, ENEA Centro Ricerche Roma Casaccia, Via Anguillarese 301, Rome, Santa Maria di Galeria 00123, Italy
| | - C. Dalmastri
- Division of Health Protection Technologies, ENEA Centro Ricerche Roma Casaccia, Via Anguillarese 301, Rome, Santa Maria di Galeria 00123, Italy
| | - I. D'Elia
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Roma, Lungotevere Thaon de Revel, 76, Rome 00196, Italy
| | - M. Gualtieri
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Bologna, Via Martiri di Monte Sole 4, Bologna 40129, Italy
| | - A. Piersanti
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Bologna, Via Martiri di Monte Sole 4, Bologna 40129, Italy
| | - G. Sannino
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Roma Casaccia, Via Anguillarese 301, Rome, Santa Maria di Galeria 00123, Italy
| | - R. Uccelli
- Division of Health Protection Technologies, ENEA Centro Ricerche Roma Casaccia, Via Anguillarese 301, Rome, Santa Maria di Galeria 00123, Italy
| | - G. Zanini
- Division of Models and Technology for Risk Reduction, ENEA Centro Ricerche Bologna, Via Martiri di Monte Sole 4, Bologna 40129, Italy
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Dalmastri C, Gastaldo L, Berini F, Marinelli F, Marcone GL. Description of the bacterial RNA polymerase inhibitor GE23077-producer Actinomadura sp. NRRL B-65521 T as Actinomadura lepetitiana sp. nov. Int J Syst Evol Microbiol 2020; 70:4782-4790. [PMID: 32701429 DOI: 10.1099/ijsem.0.004348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 11/18/2022] Open
Abstract
The filamentous actinomycete that produces the antibiotic GE23077 was isolated by the Lepetit Research Group from a soil sample collected in Thailand, and it was classified as a member of the genus Actinomadura on the basis of its morphology and cell-wall composition. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain formed a distinct monophyletic line within the genus Actinomadura, and it was most closely related to Actinomadura bangladeshensis DSM 45347T (99.31 % similarity) and Actinomadura mexicana DSM 44485T (98.94 %). The GE23077-producing strain formed an extensively branched, non-fragmented vegetative mycelium; no pseudosporangia were formed and the arthrospores were organized in slightly twisted chains. The cell wall contained meso-2,6-diaminopimelic acid and the diagnostic sugar was madurose. The predominant menaquinone was MK-9(H6), with minor amounts of MK-9(H8) and MK-9(H4). The diagnostic phospholipids were phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were C16 : 0 and tuberculostearic acid (10-methyloctadecanoic acid), followed by minor amounts of C18:1ω9c, C16:1ω7c and 10-methylheptadecanoic acid. The genomic DNA G+C content was 71.77 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, and the low DNA-DNA relatedness between the GE23077-producing strain and closely related type strains clearly demonstrate that it represents a novel species of the genus Actinomadura, for which the name Actinomadura lepetitiana sp. nov. is proposed. The type strain is NRRL B-65521T(=LMG 31258T=DSM 109019T).
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Affiliation(s)
- Claudia Dalmastri
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Department for Sustainability, C.R. Casaccia, 00123 Rome, Italy
| | - Luciano Gastaldo
- University of Insubria, Department of Biotechnology and Life Sciences, 21100 Varese, Italy
| | - Francesca Berini
- University of Insubria, Department of Biotechnology and Life Sciences, 21100 Varese, Italy
| | - Flavia Marinelli
- University of Insubria, Department of Biotechnology and Life Sciences, 21100 Varese, Italy
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Savi D, Quattrucci S, Trancassini M, Dalmastri C, De Biase RV, Maggisano M, Palange P, Bevivino A. Impact of clonally-related Burkholderia contaminans strains in two patients attending an Italian cystic fibrosis centre: a case report. BMC Pulm Med 2019; 19:164. [PMID: 31464603 PMCID: PMC6714384 DOI: 10.1186/s12890-019-0923-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 08/19/2019] [Indexed: 11/11/2022] Open
Abstract
Background Burkholderia contaminans is one of the 20 closely related bacterial of the Burkholderia cepacia complex, a group of bacteria that are ubiquitous in the environment and capable of infecting people with cystic fibrosis (CF). This species is an emerging pathogen and it has been widely isolated from CF patients in Argentina, Spain, Portugal, Australia, Canada, USA with a low prevalence in Ireland, France, Russia, Switzerland, Czech Republic, and Italy. This is the first report of B. contaminans affecting two Italian CF patients attending the same CF Centre. We correlate B. contaminans colonisation with lung function decline and co-infection with other clinically relevant CF pathogens. Case presentation B. contaminans was identified by Multi Locus Sequence Typing in routine sputum analysis of two Caucasian CF women homozygous for Phe508del CFTR mutation. Sequence Type 102 was detected in both strains. It is known that B. contaminans ST102 was isolated both from CF and non-CF patients, with an intercontinental spread across the world. Random Amplified Polymorphic DNA analysis revealed the genetic relatedness between the two strains. We examined their susceptibility to antimicrobial agents, comparing the latter with that recorded for other B. contaminans isolated from different countries. We also described key virulence factors possibly linked with a clinical outcome. Specifically, we attempted to correlate colonization with the incidence of acute exacerbation of symptoms and lung function decline. Conclusions This case presentation suggests that acquisition of B. contaminans ST102 is not directly associated with a lung function decline. We retain that the presence of other CF pathogens (i.e. MRSA and Trichosporon) along with B. contaminans ST102 might have contributed to the worsening of clinical conditions in our CF patients. The circumstances leading to the establishment of B. contaminans ST102 infections are still unknown. We highlight the importance to proper detect and typing bacteria implicated in CF infection by using molecular techniques.
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Affiliation(s)
- Daniela Savi
- Department of Public Health and Infectious Diseases, Adult Cystic Fibrosis Centre, "Sapienza" University of Rome, V.le Universita' 37, 00185, Rome, Italy. .,Cystic Fibrosis Unit, Bambino Gesù Children's Hospital, Rome, Italy.
| | - Serena Quattrucci
- Dipartimento Materno Infantile e Scienze Urologiche, Sapienza University of Rome, Rome, Italy
| | - Maria Trancassini
- Department of Public Health and Infectious Diseases, Laboratory of Microbiology, Policlinico Umberto I Hospital, Rome, Italy
| | - Claudia Dalmastri
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA C.R Casaccia, 00123, Rome, Italy
| | | | - Marta Maggisano
- Sant'Andrea Hospital, Sapienza University of Rome, Rome, Italy
| | - Paolo Palange
- Department of Public Health and Infectious Diseases, Adult Cystic Fibrosis Centre, "Sapienza" University of Rome, V.le Universita' 37, 00185, Rome, Italy
| | - Annamaria Bevivino
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA C.R Casaccia, 00123, Rome, Italy
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Daddiego L, Bianco L, Capodicasa C, Carbone F, Dalmastri C, Daroda L, Del Fiore A, De Rossi P, Di Carli M, Donini M, Lopez L, Mengoni A, Paganin P, Perrotta G, Bevivino A. Omics approaches on fresh-cut lettuce reveal global molecular responses to sodium hypochlorite and peracetic acid treatment. J Sci Food Agric 2018; 98:737-750. [PMID: 28675480 DOI: 10.1002/jsfa.8521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/26/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Lettuce is a leafy vegetable that is extensively commercialized as a ready-to-eat product because of its widespread use in human nutrition as salad. It is well known that washing treatments can severely affect the quality and shelf-life of ready-to-eat vegetables. The study presented here evaluated the effect of two washing procedures on fresh-cut lettuce during storage. RESULTS An omics approach was applied to reveal global changes at molecular level induced by peracetic acid washing in comparison with sodium hypochlorite treatment. Microbiological analyses were also performed to quantify total bacterial abundance and composition. The study revealed wide metabolic alterations induced by the two sanitizers. In particular, transcriptomic and proteomic analyses pointed out a number of transcripts and proteins differentially accumulated in response to peracetic acid washing, mainly occurring on the first day of storage. In parallel, different microbiota composition and significant reduction in total bacterial load following washing were also observed. CONCLUSION The results provide useful information for the fresh-cut industry to select an appropriate washing procedure preserving fresh-like attributes as much as possible during storage of the end product. Molecular evidence indicated peracetic acid to be a valid alternative to sodium hypochlorite as sanitizer solution. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Loretta Daddiego
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Trisaia Research Center, Rotondella, MT, Italy
| | - Linda Bianco
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Trisaia Research Center, Rotondella, MT, Italy
| | - Cristina Capodicasa
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Fabrizio Carbone
- Council for Agricultural Research and Economics (CREA), Research Centre for Olive, Citrus and Tree Fruit, Rende, (CS), Italy
| | - Claudia Dalmastri
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Lorenza Daroda
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Antonella Del Fiore
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Patrizia De Rossi
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Mariasole Di Carli
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Marcello Donini
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Loredana Lopez
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Trisaia Research Center, Rotondella, MT, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Patrizia Paganin
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Gaetano Perrotta
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Trisaia Research Center, Rotondella, MT, Italy
| | - Annamaria Bevivino
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
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Marcone GL, Binda E, Reguzzoni M, Gastaldo L, Dalmastri C, Marinelli F. Classification of Actinoplanes sp. ATCC 33076, an actinomycete that produces the glycolipodepsipeptide antibiotic ramoplanin, as Actinoplanes ramoplaninifer sp. nov. Int J Syst Evol Microbiol 2017; 67:4181-4188. [DOI: 10.1099/ijsem.0.002281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, and ‘The Protein Factory’ Research Center, Politecnico of Milano and University of Insubria, 21100 Varese, Italy
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, and ‘The Protein Factory’ Research Center, Politecnico of Milano and University of Insubria, 21100 Varese, Italy
| | - Marcella Reguzzoni
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | - Luciano Gastaldo
- Department of Biotechnology and Life Sciences, University of Insubria, and ‘The Protein Factory’ Research Center, Politecnico of Milano and University of Insubria, 21100 Varese, Italy
| | - Claudia Dalmastri
- Territorial and Production Systems Sustainability Department, ENEA (Italian National Agency for New Technologies Energy and Sustainable Economic Development), via Anguillarese 301, 00123 Rome, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, and ‘The Protein Factory’ Research Center, Politecnico of Milano and University of Insubria, 21100 Varese, Italy
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Dalmastri C, Gastaldo L, Marcone GL, Binda E, Congiu T, Marinelli F. Classification of Nonomuraea sp. ATCC 39727, an actinomycete that produces the glycopeptide antibiotic A40926, as Nonomuraea gerenzanensis sp. nov. Int J Syst Evol Microbiol 2017; 66:912-921. [PMID: 26944798 DOI: 10.1099/ijsem.0.000810] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain ATCC 39727, which produces the antibiotic A40926 (the natural precursor of the antibiotic dalbavancin), was isolated from a soil sample collected in India, and it was originally classified as a member of the genus Actinomadura on the base of morphology and cell-wall composition. A phylogenetic analysis based on 16S rRNA gene sequences indicates that the strain forms a distinct clade within the genus Nonomuraea, and it is most closely related to Nonomuraea angiospora DSM 43173T (98.72 % similarity) and Nonomuraea jabiensis A4036T (98.69 %). The strain forms an extensively branched substrate mycelium and aerial hyphae that form spiral chains of spores with ridged surfaces. The cell wall contains meso-diaminopimelic acid and the whole-cell sugars are glucose, ribose, galactose, mannose and madurose (madurose as the diagnostic sugar). The N-acyl type of muramic acid is acetyl. The predominant menaquinone is MK-9(H4), with minor amounts of MK-9(H2), MK-9(H6) and MK-9(H0). The polar-lipid profile includes diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylmethylethanolamine, phosphatidylinositol and a series of uncharacterized phospholipids, glycolipids and phosphoglycolipids. The major cellular fatty acids are iso-C16 : 0 and 10-methyl C17 : 0. The genomic DNA G+C content is 71.2 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, together with DNA-DNA relatedness between strain ATCC 39727 and closely related type strains, clearly demonstrated that strain ATCC 39727 represents a novel species of the genus Nonomuraea, for which the name Nonomuraea gerenzanensis sp. nov. is proposed. The type strain is ATCC 39727T ( = DSM 100948T).
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Affiliation(s)
- Claudia Dalmastri
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Department for Sustainability of Production and Territorial Systems, via Anguillarese 301, 00123, Rome, Italy
| | - Luciano Gastaldo
- Department of Biotechnology and Life Sciences, University of Insubria, and 'The Protein Factory' Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, 21100, Varese, Italy
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, and 'The Protein Factory' Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, 21100, Varese, Italy
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, and 'The Protein Factory' Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, 21100, Varese, Italy
| | - Terenzio Congiu
- Department of Surgical and Morphological Sciences, University of Insubria, 21100, Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, and 'The Protein Factory' Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, 21100, Varese, Italy
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Bacci G, Paganin P, Lopez L, Vanni C, Dalmastri C, Cantale C, Daddiego L, Perrotta G, Dolce D, Morelli P, Tuccio V, De Alessandri A, Fiscarelli EV, Taccetti G, Lucidi V, Bevivino A, Mengoni A. Correction: Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline. PLoS One 2016; 11:e0160726. [PMID: 27478895 PMCID: PMC4968831 DOI: 10.1371/journal.pone.0160726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0156807.].
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Bacci G, Paganin P, Lopez L, Vanni C, Dalmastri C, Cantale C, Daddiego L, Perrotta G, Dolce D, Morelli P, Tuccio V, De Alessandri A, Fiscarelli EV, Taccetti G, Lucidi V, Bevivino A, Mengoni A. Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline. PLoS One 2016; 11:e0156807. [PMID: 27355625 PMCID: PMC4927098 DOI: 10.1371/journal.pone.0156807] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 03/15/2016] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
Abstract
Chronic airway infection is a hallmark feature of cystic fibrosis (CF) disease. In the present study, sputum samples from CF patients were collected and characterized by 16S rRNA gene-targeted approach, to assess how lung microbiota composition changes following a severe decline in lung function. In particular, we compared the airway microbiota of two groups of patients with CF, i.e. patients with a substantial decline in their lung function (SD) and patients with a stable lung function (S). The two groups showed a different bacterial composition, with SD patients reporting a more heterogeneous community than the S ones. Pseudomonas was the dominant genus in both S and SD patients followed by Staphylococcus and Prevotella. Other than the classical CF pathogens and the most commonly identified non-classical genera in CF, we found the presence of the unusual anaerobic genus Sneathia. Moreover, the oligotyping analysis revealed the presence of other minor genera described in CF, highlighting the polymicrobial nature of CF infection. Finally, the analysis of correlation and anti-correlation networks showed the presence of antagonism and ecological independence between members of Pseudomonas genus and the rest of CF airways microbiota, with S patients showing a more interconnected community in S patients than in SD ones. This population structure suggests a higher resilience of S microbiota with respect to SD, which in turn may hinder the potential adverse impact of aggressive pathogens (e.g. Pseudomonas). In conclusion, our findings shed a new light on CF airway microbiota ecology, improving current knowledge about its composition and polymicrobial interactions in patients with CF.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, Florence, Italy
| | - Patrizia Paganin
- Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Loredana Lopez
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy
| | - Chiara Vanni
- Department of Biology, University of Florence, Florence, Italy
| | - Claudia Dalmastri
- Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Cristina Cantale
- Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Loretta Daddiego
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy
| | - Gaetano Perrotta
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy
| | - Daniela Dolce
- Department of Pediatrics, Cystic Fibrosis Center, Meyer Hospital, Florence, Italy
| | - Patrizia Morelli
- Department of Pediatrics, Cystic Fibrosis Center, G. Gaslini Institute, Genoa, Italy
| | - Vanessa Tuccio
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | | | - Ersilia Vita Fiscarelli
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | - Giovanni Taccetti
- Department of Pediatrics, Cystic Fibrosis Center, Meyer Hospital, Florence, Italy
| | - Vincenzina Lucidi
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
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Morales P, Wang L, Krissanaprasit A, Dalmastri C, Caruso M, De Stefano M, Mosiello L, Rapone B, Rinaldi A, Vespucci S, Vinther J, Retterer S, Gothelf KV. Suspending DNA Origami Between Four Gold Nanodots. Small 2016; 12:169-173. [PMID: 26573881 DOI: 10.1002/smll.201501782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 09/16/2015] [Indexed: 06/05/2023]
Abstract
Rectangular DNA origami functionalized with thiols in each of the four corners immobilizes by self-assembly between lithographically patterned gold nanodots on a silicon oxide surface.
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Affiliation(s)
- Piero Morales
- Centro Ricerche della Casaccia, Via Anguillarese 301, 00123, S. Maria di Galeria, Roma, Italy
| | - Liqian Wang
- Centro NAST Università di Tor Vergata, Via della Ricerca Scientifica 1, 00133, Roma, Italy
| | - Abhichart Krissanaprasit
- National Research Foundation, Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Claudia Dalmastri
- Centro Ricerche della Casaccia, Via Anguillarese 301, 00123, S. Maria di Galeria, Roma, Italy
| | - Mario Caruso
- Centro NAST Università di Tor Vergata, Via della Ricerca Scientifica 1, 00133, Roma, Italy
| | - Mattia De Stefano
- National Research Foundation, Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Lucia Mosiello
- Centro Ricerche della Casaccia, Via Anguillarese 301, 00123, S. Maria di Galeria, Roma, Italy
| | - Bruno Rapone
- Centro Ricerche della Casaccia, Via Anguillarese 301, 00123, S. Maria di Galeria, Roma, Italy
| | - Antonio Rinaldi
- Centro Ricerche della Casaccia, Via Anguillarese 301, 00123, S. Maria di Galeria, Roma, Italy
| | - Stefano Vespucci
- Centro NAST Università di Tor Vergata, Via della Ricerca Scientifica 1, 00133, Roma, Italy
| | - Jesper Vinther
- National Research Foundation, Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Scott Retterer
- Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831-6496, USA
| | - Kurt V Gothelf
- National Research Foundation, Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
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11
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Di Carli M, De Rossi P, Paganin P, Del Fiore A, Lecce F, Capodicasa C, Bianco L, Perrotta G, Mengoni A, Bacci G, Daroda L, Dalmastri C, Donini M, Bevivino A. Bacterial community and proteome analysis of fresh-cut lettuce as affected by packaging. FEMS Microbiol Lett 2016; 363:fnv209. [PMID: 26511951 DOI: 10.1093/femsle/fnv209] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2015] [Indexed: 01/11/2023] Open
Abstract
With the growing demand of fresh-cut vegetables, a variety of packaging films are produced specifically to improve safety and quality of the fresh vegetables over the storage period. The aim of our work was to evaluate the influence of different packaging films on the quality of fresh-cut lettuce analyzing changes in bacterial community composition and modifications at the proteome level, by means of culture-dependent/culture-independent methods and differential gel electrophoresis combined with mass spectrometry analysis. Total viable counts indicated the presence of a highly variable and complex microbial flora, around a mean value of 6.26 log10 CFU g(-1). Analysis of terminal-restriction fragment length polymorphism data indicated that bacterial communities changed with packaging films and time, showing differences in community composition and diversity indices between the commercially available package (F) and the new packages (A and C), in the first days after packaging. Also proteomic analysis revealed significant changes, involving proteins related to energy metabolism, photosynthesis, plant defense and oxidative stress processes, between F and A/C packages. In conclusion, microbiological and proteomic analysis have proved to be powerful tools to provide new insights into both the composition of leaf-associated bacterial communities and protein content of fresh-cut lettuce during the shelf-life storage process.
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Affiliation(s)
- Mariasole Di Carli
- Sustainable Territorial and Production Systems Department, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, 00123, Rome, Italy
| | - Patrizia De Rossi
- Sustainable Territorial and Production Systems Department, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, 00123, Rome, Italy
| | - Patrizia Paganin
- Sustainable Territorial and Production Systems Department, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, 00123, Rome, Italy
| | - Antonella Del Fiore
- Sustainable Territorial and Production Systems Department, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, 00123, Rome, Italy
| | - Francesca Lecce
- Sustainable Territorial and Production Systems Department, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, 00123, Rome, Italy
| | - Cristina Capodicasa
- Sustainable Territorial and Production Systems Department, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, 00123, Rome, Italy
| | - Linda Bianco
- Energy Technologies Department, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, 75026 Rotondella (MT), Italy
| | - Gaetano Perrotta
- Energy Technologies Department, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, 75026 Rotondella (MT), Italy
| | - Alessio Mengoni
- Biology Department, University of Florence, I-50019 Sesto F.no, Florence, Italy
| | - Giovanni Bacci
- Biology Department, University of Florence, I-50019 Sesto F.no, Florence, Italy
| | - Lorenza Daroda
- Sustainable Territorial and Production Systems Department, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, 00123, Rome, Italy
| | - Claudia Dalmastri
- Sustainable Territorial and Production Systems Department, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, 00123, Rome, Italy
| | - Marcello Donini
- Sustainable Territorial and Production Systems Department, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, 00123, Rome, Italy
| | - Annamaria Bevivino
- Sustainable Territorial and Production Systems Department, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, 00123, Rome, Italy
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12
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Papaleo MC, Fondi M, Maida I, Perrin E, Bevivino A, Dalmastri C, Fani R. Analysis of a Pool of Small Plasmids from Soil Heterotrophic Cultivable Bacterial Communities. Open Microbiol J 2015; 9:98-109. [PMID: 26464609 PMCID: PMC4598422 DOI: 10.2174/1874285801509010098] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 12/23/2014] [Accepted: 01/01/2015] [Indexed: 11/22/2022] Open
Abstract
In this work the analysis of the plasmid presence on soil aerobic cultivable heterotrophic bacterial communities was carried out checking a panel of 1,200 isolates, in order to establish the frequency of plasmid presence as well as the degree of plasmid flow between strains affiliated to the same or different taxon. Bacterial communities were isolated from two different sites of a 13-year experimental field with a clay-silt texture. Plasmid molecules were detected at low frequency (27 isolates, 2%) with a size ranging between 2 Kb and 40 Kb. The RAPD analysis performed on the plasmid-harboring isolates and the phylogenetic analysis of the whole community using the 16S rRNA gene sequences revealed the existence of transfer of the same plasmids between strains belonging to the same species and, in some cases, to different species of the same genus. As it might be expected, even though the viable cells title did not differ significantly between the two samplings, the overall data disclosed an uneven distribution of both species and plasmid-harboring strains.
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Affiliation(s)
- Maria Cristiana Papaleo
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Isabel Maida
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Elena Perrin
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Annamaria Bevivino
- Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, ENEA Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Claudia Dalmastri
- Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, ENEA Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
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13
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Paganin P, Fiscarelli EV, Tuccio V, Chiancianesi M, Bacci G, Morelli P, Dolce D, Dalmastri C, De Alessandri A, Lucidi V, Taccetti G, Mengoni A, Bevivino A. Changes in cystic fibrosis airway microbial community associated with a severe decline in lung function. PLoS One 2015; 10:e0124348. [PMID: 25898134 PMCID: PMC4405530 DOI: 10.1371/journal.pone.0124348] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [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: 09/25/2014] [Accepted: 03/01/2015] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease resulting in chronic polymicrobial infections of the airways and progressive decline in lung function. To gain insight into the underlying causes of severe lung diseases, we aimed at comparing the airway microbiota detected in sputum of CF patients with stable lung function (S) versus those with a substantial decline in lung function (SD). Microbiota composition was investigated by using culture-based and culture-independent methods, and by performing multivariate and statistical analyses. Culture-based methods identified some microbial species associated with a worse lung function, i.e. Pseudomonas aeruginosa, Rothia mucilaginosa, Streptococcus pneumoniae and Candida albicans, but only the presence of S. pneumoniae and R. mucilaginosa was found to be associated with increased severe decline in forced expiratory volume in 1 second (FEV1). Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis revealed a higher bacterial diversity than that detected by culture-based methods. Molecular signatures with a statistically significant odds ratio for SD status were detected, and classified as Pseudomonas, Burkholderia and Shewanella, while for other Terminal Restriction Fragments (T-RFs) no species assignation was achieved. The analysis of T-RFLP data using ecological biodiversity indices showed reduced Evenness in SD patients compared to S ones, suggesting an impaired ecology of the bacterial community in SD patients. Statistically significant differences of the ecological biodiversity indices among the three sub-groups of FEV1 (normal/mild vs moderate vs severe) were also found, suggesting that the patients with moderate lung disease experienced changes in the airway assembly of taxa. Overall, changes in CF airway microbial community associated with a severe lung function decline were detected, allowing us to define some discriminatory species as well as some discriminatory T-RFs that represent good candidates for the development of predictive biomarkers of substantial decline in lung function.
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Affiliation(s)
- Patrizia Paganin
- Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
| | - Ersilia Vita Fiscarelli
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | - Vanessa Tuccio
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | | | - Giovanni Bacci
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Patrizia Morelli
- Department of Pediatrics, Cystic Fibrosis Center, G. Gaslini Institute, Genoa, Italy
| | - Daniela Dolce
- Department of Pediatrics, Cystic Fibrosis Center, Meyer Hospital, Florence, Italy
| | - Claudia Dalmastri
- Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
| | | | - Vincenzina Lucidi
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | - Giovanni Taccetti
- Department of Pediatrics, Cystic Fibrosis Center, Meyer Hospital, Florence, Italy
| | - Alessio Mengoni
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Annamaria Bevivino
- Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
- * E-mail:
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14
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Bevivino A, Paganin P, Bacci G, Florio A, Pellicer MS, Papaleo MC, Mengoni A, Ledda L, Fani R, Benedetti A, Dalmastri C. Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region. PLoS One 2014; 9:e105515. [PMID: 25144665 PMCID: PMC4140800 DOI: 10.1371/journal.pone.0105515] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [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: 05/24/2014] [Accepted: 07/23/2014] [Indexed: 11/18/2022] Open
Abstract
Land-use change is considered likely to be one of main drivers of biodiversity changes in grassland ecosystems. To gain insight into the impact of land use on the underlying soil bacterial communities, we aimed at determining the effects of agricultural management, along with seasonal variations, on soil bacterial community in a Mediterranean ecosystem where different land-use and plant cover types led to the creation of a soil and vegetation gradient. A set of soils subjected to different anthropogenic impact in a typical Mediterranean landscape, dominated by Quercus suber L., was examined in spring and autumn: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards (ploughed and grass covered). Land uses affected the chemical and structural composition of the most stabilised fractions of soil organic matter and reduced soil C stocks and labile organic matter at both sampling season. A significant effect of land uses on bacterial community structure as well as an interaction effect between land uses and season was revealed by the EP index. Cluster analysis of culture-dependent DGGE patterns showed a different seasonal distribution of soil bacterial populations with subgroups associated to different land uses, in agreement with culture-independent T-RFLP results. Soils subjected to low human inputs (cork-oak forest and pasture) showed a more stable bacterial community than those with high human input (vineyards and managed meadow). Phylogenetic analysis revealed the predominance of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes phyla with differences in class composition across the site, suggesting that the microbial composition changes in response to land uses. Taken altogether, our data suggest that soil bacterial communities were seasonally distinct and exhibited compositional shifts that tracked with changes in land use and soil management. These findings may contribute to future searches for bacterial bio-indicators of soil health and sustainable productivity.
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Affiliation(s)
- Annamaria Bevivino
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development) Casaccia Research Center, Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Rome, Italy
- * E-mail:
| | - Patrizia Paganin
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development) Casaccia Research Center, Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Rome, Italy
| | - Giovanni Bacci
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Research Centre for the Soil-Plant System, Rome, Italy
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy
| | - Alessandro Florio
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Research Centre for the Soil-Plant System, Rome, Italy
| | - Maite Sampedro Pellicer
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development) Casaccia Research Center, Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Rome, Italy
| | - Maria Cristiana Papaleo
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy
| | - Alessio Mengoni
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy
| | - Luigi Ledda
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy
| | - Anna Benedetti
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Research Centre for the Soil-Plant System, Rome, Italy
| | - Claudia Dalmastri
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development) Casaccia Research Center, Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Rome, Italy
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15
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Paganin P, Chiarini L, Bevivino A, Dalmastri C, Farcomeni A, Izzo G, Signorini A, Varrone C, Tabacchioni S. Vertical distribution of bacterioplankton in Lake Averno in relation to water chemistry. FEMS Microbiol Ecol 2012; 84:176-88. [DOI: 10.1111/1574-6941.12048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 10/24/2012] [Accepted: 11/22/2012] [Indexed: 11/26/2022] Open
Affiliation(s)
- Patrizia Paganin
- ENEA C. R. Casaccia; Technical Unit for Sustainable Development and Innovation of Agroindustrial System; Rome; Italy
| | - Luigi Chiarini
- ENEA C. R. Casaccia; Technical Unit for Sustainable Development and Innovation of Agroindustrial System; Rome; Italy
| | - Annamaria Bevivino
- ENEA C. R. Casaccia; Technical Unit for Sustainable Development and Innovation of Agroindustrial System; Rome; Italy
| | - Claudia Dalmastri
- ENEA C. R. Casaccia; Technical Unit for Sustainable Development and Innovation of Agroindustrial System; Rome; Italy
| | - Alessio Farcomeni
- Department of Public Health and Infectious Diseases; Statistics Section; Sapienza - University of Rome; Rome; Italy
| | - Giulio Izzo
- ENEA C. R. Casaccia; Technical Unit for Renewable Energy Resources; Rome; Italy
| | - Antonella Signorini
- ENEA C. R. Casaccia; Technical Unit for Renewable Energy Resources; Rome; Italy
| | - Cristiano Varrone
- ENEA C. R. Casaccia; Technical Unit for Renewable Energy Resources; Rome; Italy
| | - Silvia Tabacchioni
- ENEA C. R. Casaccia; Technical Unit for Sustainable Development and Innovation of Agroindustrial System; Rome; Italy
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16
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Bragonzi A, Farulla I, Paroni M, Twomey KB, Pirone L, Lorè NI, Bianconi I, Dalmastri C, Ryan RP, Bevivino A. Modelling co-infection of the cystic fibrosis lung by Pseudomonas aeruginosa and Burkholderia cenocepacia reveals influences on biofilm formation and host response. PLoS One 2012; 7:e52330. [PMID: 23284990 PMCID: PMC3528780 DOI: 10.1371/journal.pone.0052330] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/12/2012] [Indexed: 02/07/2023] Open
Abstract
The Gram-negative bacteria Pseudomonas aeruginosa and Burkholderia cenocepacia are opportunistic human pathogens that are responsible for severe nosocomial infections in immunocompromised patients and those suffering from cystic fibrosis (CF). These two bacteria have been shown to form biofilms in the airways of CF patients that make such infections more difficult to treat. Only recently have scientists begun to appreciate the complicated interplay between microorganisms during polymicrobial infection of the CF airway and the implications they may have for disease prognosis and response to therapy. To gain insight into the possible role that interaction between strains of P. aeruginosa and B. cenocepacia may play during infection, we characterised co-inoculations of in vivo and in vitro infection models. Co-inoculations were examined in an in vitro biofilm model and in a murine model of chronic infection. Assessment of biofilm formation showed that B. cenocepacia positively influenced P. aeruginosa biofilm development by increasing biomass. Interestingly, co-infection experiments in the mouse model revealed that P. aeruginosa did not change its ability to establish chronic infection in the presence of B. cenocepacia but co-infection did appear to increase host inflammatory response. Taken together, these results indicate that the co-infection of P. aeruginosa and B. cenocepacia leads to increased biofilm formation and increased host inflammatory response in the mouse model of chronic infection. These observations suggest that alteration of bacterial behavior due to interspecies interactions may be important for disease progression and persistent infection.
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Affiliation(s)
- Alessandra Bragonzi
- Division of Immunology, Transplantation and Infectious Diseases, Infections and Cystic Fibrosis Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Ilaria Farulla
- Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, ENEA Casaccia Research Centre, Rome, Italy
| | - Moira Paroni
- Division of Immunology, Transplantation and Infectious Diseases, Infections and Cystic Fibrosis Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Kate B. Twomey
- Department of Microbiology, BioSciences Institute, University College Cork, Cork, Ireland
| | - Luisa Pirone
- Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, ENEA Casaccia Research Centre, Rome, Italy
| | - Nicola Ivan Lorè
- Division of Immunology, Transplantation and Infectious Diseases, Infections and Cystic Fibrosis Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Irene Bianconi
- Division of Immunology, Transplantation and Infectious Diseases, Infections and Cystic Fibrosis Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Claudia Dalmastri
- Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, ENEA Casaccia Research Centre, Rome, Italy
| | - Robert P. Ryan
- Department of Microbiology, BioSciences Institute, University College Cork, Cork, Ireland
| | - Annamaria Bevivino
- Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, ENEA Casaccia Research Centre, Rome, Italy
- * E-mail:
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17
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Bevivino A, Pirone L, Pilkington R, Cifani N, Dalmastri C, Callaghan M, Ascenzioni F, McClean S. WS11.6 Environmental Burkholderia cenocepacia strains can disrupt epithelial integrity in bronchial epithelial cells in vitro and have a more profound effect on ZO-1 in CF cells. J Cyst Fibros 2012. [DOI: 10.1016/s1569-1993(12)60080-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Bevivino A, Pirone L, Pilkington R, Cifani N, Dalmastri C, Callaghan M, Ascenzioni F, McClean S. Interaction of environmental Burkholderia cenocepacia strains with cystic fibrosis and non-cystic fibrosis bronchial epithelial cells in vitro. Microbiology (Reading) 2012; 158:1325-1333. [PMID: 22322958 DOI: 10.1099/mic.0.056986-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Burkholderia cenocepacia is an important human pathogen in patients with cystic fibrosis (CF). Non-clinical reservoirs may play a role in the acquisition of infection, so it is important to evaluate the pathogenic potential of environmental B. cenocepacia isolates. In this study, we investigated the interactions of two environmental B. cenocepacia strains (Mex1 and MCII-168) with two bronchial epithelial cell lines, 16HBE14o(-) and CFBE41o(-), which have a non-CF and a CF phenotype, respectively. The environmental strains showed a significantly lower level of invasion into both CF and non-CF cells in comparison with the clinical B. cenocepacia LMG16656(T) strain. Exposure of polarized CFBE41o(-) or 16HBE14o(-) cells to the environmental strains resulted in a significant reduction in transepithelial resistance (TER), comparable with that observed following exposure to the clinical strain. A different mechanism of tight junction disruption in CF versus non-CF epithelia was found. In the 16HBE41o(-) cells, the environmental strains resulted in a drop in TER without any apparent effect on tight junction proteins such as zonula occludens-1 (ZO-1). In contrast, in CF cells, the amount of ZO-1 and its localization were clearly altered by the presence of both the environmental strains, comparable with the effect of LMG16656. This study demonstrates that even if the environmental strains are significantly less invasive than the clinical strain, they have an effect on epithelial integrity comparable with that of the clinical strain. Finally, the tight junction regulatory protein ZO-1 appears to be more susceptible to the presence of environmental strains in CF cells than in cells which express a functional cystic fibrosis transmembrane regulator (CFTR).
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Affiliation(s)
- Annamaria Bevivino
- ENEA C.R. Casaccia - Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Via Anguillarese 301, 00123 Rome, Italy
| | - Luisa Pirone
- Department of Biology and Biotechnology 'C. Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy.,ENEA C.R. Casaccia - Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Via Anguillarese 301, 00123 Rome, Italy
| | - Ruth Pilkington
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Old Blessington Road, Dublin 2, Ireland
| | - Noemi Cifani
- Department of Biology and Biotechnology 'C. Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Claudia Dalmastri
- ENEA C.R. Casaccia - Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Via Anguillarese 301, 00123 Rome, Italy
| | - Máire Callaghan
- Centre of Applied Science for Health, Institute of Technology Tallaght, Old Blessington Road, Dublin 2, Ireland.,Centre of Microbial Host Interactions, Institute of Technology Tallaght, Old Blessington Road, Dublin 2, Ireland
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology 'C. Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Siobhán McClean
- Centre of Applied Science for Health, Institute of Technology Tallaght, Old Blessington Road, Dublin 2, Ireland.,Centre of Microbial Host Interactions, Institute of Technology Tallaght, Old Blessington Road, Dublin 2, Ireland
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19
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Bevivino A, Costa B, Cantale C, Cesarini S, Chiarini L, Tabacchioni S, Caballero-Mellado J, Dalmastri C. Genetic relationships among Italian and Mexican maize-rhizosphere Burkholderia cepacia complex (BCC) populations belonging to Burkholderia cenocepacia IIIB and BCC6 group. BMC Microbiol 2011; 11:228. [PMID: 21995705 PMCID: PMC3377929 DOI: 10.1186/1471-2180-11-228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 10/13/2011] [Indexed: 11/25/2022] Open
Abstract
Background A close association between maize roots and Burkholderia cepacia complex (BCC) bacteria has been observed in different locations globally. In this study we investigated by MultiLocus Restriction Typing (MLRT) the genetic diversity and relationships among Burkholderia cenocepacia IIIB and BCC6 populations associated with roots of maize plants cultivated in geographically distant countries (Italy and Mexico), in order to provide new insights into their population structure, evolution and ecology. Results The 31 B. cenocepacia IIIB and 65 BCC6 isolates gave rise to 29 and 39 different restriction types (RTs), respectively. Two pairs of isolates of B. cenocepacia IIIB and BCC6, recovered from both Italian and Mexican maize rhizospheres, were found to share the same RT. The eBURST (Based Upon Related Sequence Types) analysis of MLRT data grouped all the B. cenocepacia IIIB isolates into four clonal complexes, with the RT-4-complex including the 42% of them, while the majority of the BCC6 isolates (94%) were grouped into the RT-104-complex. These two main clonal complexes included RTs shared by both Italian and Mexican maize rhizospheres and a clear relationship between grouping and maize variety was also found. Grouping established by eBURST correlated well with the assessment using unweighted-pair group method with arithmetic mean (UPGMA). The standardized index of association values obtained in both B. cenocepacia IIIB and BCC6 suggests an epidemic population structure in which occasional clones emerge and spread. Conclusions Taken together our data demonstrate a wide dispersal of certain B. cenocepacia IIIB and BCC6 isolates in Mexican and Italian maize rhizospheres. Despite the clear relationship found between the geographic origin of isolates and grouping, identical RTs and closely related isolates were observed in geographically distant regions. Ecological factors and selective pressure may preferably promote some genotypes within each local microbial population, favouring the spread of a single clone above the rest of the recombinant population.
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Affiliation(s)
- Annamaria Bevivino
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Development) Casaccia Research Center-Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Via Anguillarese 301, 00123 S, Maria di Galeria, Rome, Italy.
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Paganin P, Pellicer MS, Ledda L, Bagella S, Madrau S, Papaleo M, Fani R, Dalmastri C, Bevivino A. Soil microbial community response to differences in soil managements and seasonal changes. J Biotechnol 2010. [DOI: 10.1016/j.jbiotec.2010.09.235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ferri L, Perrin E, Campana S, Tabacchioni S, Taccetti G, Cocchi P, Ravenni N, Dalmastri C, Chiarini L, Bevivino A, Manno G, Mentasti M, Fani R. Application of multiplex single nucleotide primer extension (mSNuPE) to the identification of bacteria: the Burkholderia cepacia complex case. J Microbiol Methods 2010; 80:251-6. [PMID: 20079386 DOI: 10.1016/j.mimet.2010.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Accepted: 01/06/2010] [Indexed: 10/20/2022]
Abstract
Burkholderia cepacia complex (BCC) is characterized by a complex taxonomy constituted by seventeen closely related species of both biotechnological and clinical importance. Several molecular methods have been developed to accurately identify BCC species but simpler and effective strategies for BCC classification are still needed. A single nucleotide primer extension (SNuPE) assay using gyrB as a target gene was developed to identify bacteria belonging to the B. cepacia (BCC) complex. This technique allows the successful detection and distinction of single nucleotide polymorphisms (SNPs) and is effectively applied in routine medical diagnosis since it permits to analyze routinely many samples in a few times. Seven SNuPE primers were designed analyzing the conserved regions of the BCC gyrB sequences currently available in databases. The specificity of the assay was evaluated using reference strains of some BCC species. Data obtained enabled to discriminate bacteria belonging to the species B. multivorans, B. cenocepacia (including bacteria belonging to recA lineages III-A, III-C, and III-D), B. vietnamiensis, B. dolosa, B. ambifaria, B. anthina and B. pyrrocinia. Conversely, identification failed for B. cepacia, B. cenocepacia III-B and B. stabilis. This study demonstrates the efficacy of SNuPE technique for the identification of bacteria characterized by a complex taxonomical organization as BCC bacteria.
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Affiliation(s)
- L Ferri
- Department of Evolutionary Biology, University of Florence, Via Romana 17-19, I-50125 Florence, Italy
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Dalmastri C, Fiore A, Alisi C, Bevivino A, Tabacchioni S, Giuliano G, Sprocati AR, Segre L, Mahenthiralingam E, Chiarini L, Vandamme P. A rhizospheric Burkholderia cepacia complex population: genotypic and phenotypic diversity of Burkholderia cenocepacia and Burkholderia ambifaria. FEMS Microbiol Ecol 2009; 46:179-87. [PMID: 19719571 DOI: 10.1016/s0168-6496(03)00211-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The Burkholderia cepacia'complex' (Bcc) presently comprises nine species and genomovars. In order to acquire a better comprehension of the species and genomovar distribution and of the genetic diversity among environmental Bcc bacteria, a natural population of 60 bacterial isolates recovered from the rhizosphere of maize and belonging to the Bcc has been characterised to assess the exact taxonomic position, the genetic polymorphism and the metabolic profiles of isolates. The identification of the different species and genomovars was accomplished by a combination of techniques including sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins and recA-based restriction fragment length polymorphism analyses. The genetic diversity among Bcc isolates was analysed by means of the random amplified polymorphic DNA and amplified fragment length polymorphism techniques; the analysis of molecular variance method was applied to estimate the genetic differences among the various species and genomovars identified within the bacterial population. Metabolic profiles based on carbon source utilisation were obtained by means of the Biolog GN assay and analysed by means of cluster analysis. Forty-four strains were identified as B. ambifaria, 11 as B. cenocepacia recA lineage III-B, four as B. pyrrocinia, and one as B. cepacia genomovar I. Marked genetic differences were observed between B. cenocepacia and B. ambifaria, whereas limited differences were found between B. pyrrocinia and B. ambifaria and between B. pyrrocinia and B. cenocepacia. No significant differences (P>0.05) were observed between the mean genetic distances of isolates belonging to B. cenocepacia, B. ambifaria, and B. pyrrocinia. Phenotypic analyses revealed that all isolates tested were able to utilise more than 75% of substrates. The highest variability in the number of utilised substrates was found among B. cenocepacia isolates, whereas the lowest was found among B. ambifaria isolates. Cluster analysis of metabolic profiles revealed pronounced differences between B. cenocepacia and B. ambifaria; in contrast, B. pyrrocinia could not be clearly separated either from B. cenocepacia or from B. ambifaria.
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Affiliation(s)
- Claudia Dalmastri
- ENEA (Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente) C.R. Casaccia, Unità Biotecnologie e Protezione della Salute e degli Ecosistemi, Via Anguillarese 301, 00060 S. Maria di Galeria, Rome, Italy
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Cesarini S, Bevivino A, Tabacchioni S, Chiarini L, Dalmastri C. RecAgene sequence and Multilocus Sequence Typing for species-level resolution ofBurkholderia cepaciacomplex isolates. Lett Appl Microbiol 2009; 49:580-8. [DOI: 10.1111/j.1472-765x.2009.02709.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Pirone L, Bragonzi A, Farcomeni A, Paroni M, Auriche C, Conese M, Chiarini L, Dalmastri C, Bevivino A, Ascenzioni F. Burkholderia cenocepacia strains isolated from cystic fibrosis patients are apparently more invasive and more virulent than rhizosphere strains. Environ Microbiol 2008; 10:2773-84. [PMID: 18643926 DOI: 10.1111/j.1462-2920.2008.01697.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Given the widespread presence of Burkholderia cenocepacia in the rhizosphere it is important to determine whether rhizosphere strains are pathogenic for cystic fibrosis patients or not. Eighteen B. cenocepacia strains of rhizosphere and clinical origin were typed by multi-locus sequence typing (MLST) analysis and compared for their ability to invade pulmonary epithelial cells and their virulence in a mouse model of airway infection. Although there was great variability, clinical strains were the most invasive in vitro. Almost all the rhizosphere and two clinical strains were defined as non-invasive, six clinical strains as invasive, and two strains of both clinical and environmental origin as indeterminate. Exposure of murine airways to clinical strains caused higher acute mortality than that seen after challenge with rhizosphere strains. Furthermore, both clinical and environmental strains were able to persist in the lungs of infected mice, with no significant differences in bacterial loads and localization 14 days after challenge. DNA dot blot analyses of AHL synthase, porin and amidase genes, which play a role in B. cenocepacia virulence, showed that they were present in B. cenocepacia strains irrespective of their origin. Overall, our results suggest that rhizosphere strains do not differ from clinical strains in some pathogenic traits.
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Affiliation(s)
- Luisa Pirone
- ENEA C.R. Casaccia - Department of Biotechnologies, Agroindustry and Protection of Health, Plant Genetics and Genomics Section, Rome, Italy
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Dalmastri C, Baldwin A, Tabacchioni S, Bevivino A, Mahenthiralingam E, Chiarini L, Dowson C. Investigating Burkholderia cepacia complex populations recovered from Italian maize rhizosphere by multilocus sequence typing. Environ Microbiol 2008; 9:1632-9. [PMID: 17564598 DOI: 10.1111/j.1462-2920.2007.01273.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [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: 11/30/2022]
Abstract
The Burkholderia cepacia complex (BCC) comprises at least nine closely related species of abundant environmental microorganisms. Some of these species are highly spread in the rhizosphere of several crop plants, particularly of maize; additionally, as opportunistic pathogens, strains of the BCC are capable of colonizing humans. We have developed and validated a multilocus sequence typing (MLST) scheme for the BCC. Although widely applied to understand the epidemiology of bacterial pathogens, MLST has seen limited application to the population analysis of species residing in the natural environment; we describe its novel application to BCC populations within maize rhizospheres. 115 BCC isolates were recovered from the roots of different maize cultivars from three different Italian regions over a 9-year period (1994-2002). A total of 44 sequence types (STs) were found of which 41 were novel when compared with existing MLST data which encompassed a global database of 1000 clinical and environmental strains representing nearly 400 STs. In this study of rhizosphere isolates approximately 2.5 isolates per ST was found, comparable to that found for the whole BCC population. Multilocus sequence typing also resolved inaccuracies associated with previous identification of the maize isolates based on recA gene restriction fragment length polymorphims and species-specific polymerase chain reaction. The 115 maize isolates comprised the following BCC species groups, B. ambifaria (39%), BCC6 (29%), BCC5 (10%), B. pyrrocinia (8%), B. cenocepacia IIIB (7%) and B. cepacia (6%), with BCC5 and BCC6 potentially constituting novel species groups within the complex. Closely related clonal complexes of strains were identified within B. cepacia, B. cenocepacia IIIB, BCC5 and BCC6, with one of the BCC5 clonal complexes being distributed across all three sampling sites. Overall, our analysis demonstrates that the maize rhizosphere harbours a massive diversity of novel BCC STs, so that their addition to our global MLST database increased the ST diversity by 10%.
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Affiliation(s)
- Claudia Dalmastri
- ENEA C. R. Casaccia - Department of Biotechnologies, Protection of Health and Ecosystems, Rome, Italy
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26
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Tabacchioni S, Ferri L, Manno G, Mentasti M, Cocchi P, Campana S, Ravenni N, Taccetti G, Dalmastri C, Chiarini L, Bevivino A, Fani R. Use of the gyrB gene to discriminate among species of the Burkholderia cepacia complex. FEMS Microbiol Lett 2008; 281:175-82. [PMID: 18312571 DOI: 10.1111/j.1574-6968.2008.01105.x] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Bacteria of the Burkholderia cepacia complex (Bcc) are opportunistic pathogens that can cause serious infections in lungs of cystic fibrosis patients. The Bcc comprises at least nine species that have been discriminated by a polyphasic taxonomic approach. In this study, we focused on the gyrB gene, universally distributed among bacteria, as a new target gene to discriminate among the Bcc species. New PCR primers were designed to amplify a gyrB DNA fragment of about 1900 bp from 76 strains representative of all Bcc species. Nucleotide sequences of PCR products were determined and showed more than 400 polymorphic sites with high sequence similarity values from most isolates of the same species. Phylogenetic tree analysis revealed that most of the 76 gyrB sequences grouped, forming clusters, each corresponding to a given Bcc species.
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Affiliation(s)
- Silvia Tabacchioni
- ENEA - CRE - CASACCIA -Department of Biotechnologies, Agroindustry, Protection of Health - Plant genetics and Genomics Section, S. Maria di Galeria, Rome, Italy
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27
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Baldwin A, Mahenthiralingam E, Drevinek P, Vandamme P, Govan JR, Waine DJ, LiPuma JJ, Chiarini L, Dalmastri C, Henry DA, Speert DP, Honeybourne D, Maiden MCJ, Dowson CG. Environmental Burkholderia cepacia complex isolates in human infections. Emerg Infect Dis 2007; 13:458-61. [PMID: 17552100 PMCID: PMC2725883 DOI: 10.3201/eid1303.060403] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [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] [Indexed: 11/21/2022] Open
Abstract
Members of the Burkholderia cepacia complex (Bcc), found in many environments, are associated with clinical infections. Examining diverse species and strains from different environments with multilocus sequence typing, we identified >20% of 381 clinical isolates as indistinguishable from those in the environment. This finding links the natural environment with the emergence of many Bcc infections.
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Affiliation(s)
- Adam Baldwin
- Warwick University, Coventry, Wales, United Kingdom
| | | | | | | | - John R. Govan
- University of Edinburgh Medical School, Edinburgh, Scotland, United Kingdom
| | | | - John J. LiPuma
- University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Luigi Chiarini
- Ente per le Nuove Tecnologie l’Energia e l’Ambiente Casaccia, Rome, Italy
| | - Claudia Dalmastri
- Ente per le Nuove Tecnologie l’Energia e l’Ambiente Casaccia, Rome, Italy
| | - Deborah A. Henry
- University of British Columbia, Vancouver, British Columbia, Canada
| | - David P. Speert
- University of British Columbia, Vancouver, British Columbia, Canada
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Chiarini L, Bevivino A, Dalmastri C, Tabacchioni S, Visca P. Burkholderia cepacia complex species: health hazards and biotechnological potential. Trends Microbiol 2006; 14:277-86. [PMID: 16684604 DOI: 10.1016/j.tim.2006.04.006] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 03/20/2006] [Accepted: 04/21/2006] [Indexed: 10/24/2022]
Abstract
The Burkholderia cepacia complex is a group of nine closely related bacterial species that have useful properties in the natural environment as plant pest antagonists, plant growth promoters and degradative agents of toxic substances. Because these species are human opportunistic pathogens, especially in cystic fibrosis patients, biotechnological applications that involve environmental releases have been severely restricted. Recent progress in understanding the taxonomy, epidemiology and ecology of the B. cepacia complex species has unravelled considerable variability in their pathogenicity and ecological properties, which has set the basis for a reassessment of the risk posed by individual species to human health.
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Affiliation(s)
- Luigi Chiarini
- Department of Biotechnology, Protection of Health and Ecosystems, C.R. Casaccia, ENEA, 00060 Rome, Italy.
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Pirone L, Chiarini L, Dalmastri C, Bevivino A, Tabacchioni S. Detection of cultured and uncultured Burkholderia cepacia complex bacteria naturally occurring in the maize rhizosphere. Environ Microbiol 2006; 7:1734-42. [PMID: 16232288 DOI: 10.1111/j.1462-2920.2005.00897.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [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: 11/28/2022]
Abstract
The species composition of a Burkholderia cepacia complex population naturally occurring in the maize rhizosphere was investigated by using both culture-dependent and culture-independent methods. B. cepacia complex isolates were recovered from maize root slurry on the two selective media Pseudomonas cepacia azelaic acid tryptamine (PCAT) and trypan blue tetracycline (TB-T) and subjected to identification by a combination of restriction fragment length polymorphism (RFLP) analysis and species-specific polymerase chain reaction (PCR) tests of the recA gene. DNA extracted directly from root slurry was examined by means of nested PCR to amplify recA gene with species-specific B. cepacia complex primers and to obtain a library of PCR amplified recA genes. Using the culture-dependent method the species Burkholderia cepacia, Burkholderia cenocepacia, Burkholderia ambifaria and Burkholderia pyrrocinia were identified, whereas using the culture-independent method also the species Burkholderia vietnamiensis was detected. The latter method also allowed us to highlight a higher diversity within the B. cenocepacia species. In fact, by using the culture-independent method the species B. cenocepacia recA lineages IIIA and IIID besides B. cenocepacia recA lineage IIIB were detected. Moreover, higher heterogeneity of recA RFLP patterns was observed among clones assigned to the species B. cenocepacia than among B. cenocepacia isolates from selective media.
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Affiliation(s)
- Luisa Pirone
- ENEA (Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente) C.R. Casaccia, UTS Biotecnologie - Protezione della Salute e degli Ecosistemi, Sezione Genetica e Genomica, Via Anguillarese 301, 00060 S. Maria di Galeria, Rome, Italy
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Nacamulli C, Bevivino A, Dalmastri C, Tabacchioni S, Chiarini L. Perturbation of maize rhizosphere microflora following seed bacterization with Burkholderia cepacia MCI 7. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00401.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Bevivino A, Peggion V, Chiarini L, Tabacchioni S, Cantale C, Dalmastri C. Effect of Fusarium verticillioides on maize-root-associated Burkholderia cenocepacia populations. Res Microbiol 2005; 156:974-83. [PMID: 16085398 DOI: 10.1016/j.resmic.2005.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2005] [Revised: 05/09/2005] [Accepted: 05/10/2005] [Indexed: 11/24/2022]
Abstract
Burkholderia cepacia complex (Bcc) bacteria are naturally present in the rhizosphere of several crop plants and have been found to antagonize a wide range of important plant pathogens. In this study, we evaluated the effect of the pathogenic fungus Fusarium verticillioides on Bcc populations recovered from the roots of Zea mays plants. Maize plants were cultivated under greenhouse conditions and bacterial colonies were randomly isolated from distinct root portions of Fusarium-treated and control plants. We obtained a total of 120 Bcc isolates which all belonged to the species Burkholderia cenocepacia, a species of the Bcc widely distributed in natural habitats such as the rhizosphere of several crop plants. Results obtained revealed that the presence of the plant pathogen F. verticillioides had an effect at the root colonization level of B. cenocepacia populations, since an increase in indigenous B. cenocepacia bacteria was found in the rhizospheres of maize plants grown in infested soil, compared to the rhizospheres of control plants. The analysis of diversity indices as well as the investigation of genetic polymorphism of B. cenocepacia strains, isolated from Fusarium-treated and control root portions, revealed greater genetic variability in the presence of F. verticillioides, especially in the terminal root system portion. Finally, all B. cenocepacia isolates were also tested for in vitro inhibition of F. verticillioides growth as a functional property. Our results revealed that all B. cenocepacia isolates were able to restrict in vitro fungal growth, suggesting that there was no relationship between genetic polymorphism and biocontrol traits.
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Affiliation(s)
- Annamaria Bevivino
- ENEA C.R. Casaccia, Department of Biotechnologies, Protection of Health and Ecosystems, Plant genetics and Genomics Section, Via Anguillarese 301, 00060 S. Maria di Galeria, Rome, Italy.
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Alisi C, Lasinio GJ, Dalmastri C, Sprocati A, Tabacchioni S, Bevivino A, Chiarini L. Metabolic profiling of Burkholderia cenocepacia, Burkholderia ambifaria, and Burkholderia pyrrocinia isolates from maize rhizosphere. Microb Ecol 2005; 50:385-95. [PMID: 16328653 DOI: 10.1007/s00248-005-0223-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Accepted: 01/27/2005] [Indexed: 05/05/2023]
Abstract
Burkholderia cenocepacia, Burkholderia ambifaria, and Burkholderia pyrrocinia are the Burkholderia cepacia complex (Bcc) species most frequently associated with roots of crop plants. To investigate the ecophysiological diversity of these species, metabolic profiling of maize rhizosphere isolates was carried out by means of the Biolog system, using GN2 and SFN2 plates and different parameters related to optical density (OD). The metabolic profiles produced by the SFN2 and GN2 plates were identical, but the SFN2's narrower range of OD values and significantly longer reaction times made these plates less suitable for differentiation of isolates. Principal component analysis of maximum OD (ODM) and maximum substrate oxidation rate (muM) data generated by GN2 plates allowed the selection of a reduced number of carbon sources. Statistical analysis of ODM values highlighted marked differences between the metabolic profiles of B. cenocepacia and B. ambifaria, whereas metabolic profiles of B. pyrrocinia clustered very often with those of B. cenocepacia. Analysis of the mu(M) parameter resulted in a slightly lower differentiation among the three Bcc species and a higher metabolic diversity within the single species, in particular within B. cenocepacia. Finally, B. cenocepacia and B. pyrrocinia showed generally higher oxidation rates than B. ambifaria on those GN2 substrates that commonly occur in maize root exudates.
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Affiliation(s)
- Chiara Alisi
- Unità Protezione dell'Ambiente, Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente (ENEA) C. R. Casaccia, Rome, Italy
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Dalmastri C, Pirone L, Tabacchioni S, Bevivino A, Chiarini L. Efficacy of species-specificrecAPCR tests in the identification ofBurkholderia cepaciacomplex environmental isolates. FEMS Microbiol Lett 2005; 246:39-45. [PMID: 15869960 DOI: 10.1016/j.femsle.2005.03.041] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Revised: 02/25/2005] [Accepted: 03/21/2005] [Indexed: 11/16/2022] Open
Abstract
In this study, we evaluated if recA species-specific PCR assays could be successfully applied to identify environmental isolates of the widespread Burkholderia cepacia complex (Bcc) species. A total of 729 Bcc rhizosphere isolates collected in different samplings were assigned to the species B. cepacia genomovar I (61), B. cenocepacia recA lineage IIIB (514), B. ambifaria (124) and B. pyrrocinia (30), by means of recA (RFLP) analysis, and PCR tests were performed to assess sensitivity and specificity of recA species-specific primers pairs. B. cepacia genomovar I specific primers produced the expected amplicon with all isolates of the corresponding species (sensitivity, 100%), and cross-reacted with all B. pyrrocinia isolates. On the contrary, B. cenocepacia IIIB primers did not give the expected amplicon in 164 B. cenocepacia IIIB isolates (sensitivity, 68.1%), and isolates of distinct populations showed different sensitivity. B. ambifaria primers failed to amplify a recA-specific fragment only in a few isolates of this species (sensitivity, 93.5%). The absence of specific amplification in a high number of B. cenocepacia rhizosphere isolates indicates that recA specific PCR assays can lead to an underestimation of environmental microorganisms belonging to this bacterial species.
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Affiliation(s)
- Claudia Dalmastri
- Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente (ENEA), C.R. Casaccia Department of Biotechnologies, Protection of Health and Ecosystems, Plant Genetics and Genomics Section, Rome, Italy.
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Chiarini L, Cescutti P, Drigo L, Impallomeni G, Herasimenka Y, Bevivino A, Dalmastri C, Tabacchioni S, Manno G, Zanetti F, Rizzo R. Exopolysaccharides produced by Burkholderia cenocepacia recA lineages IIIA and IIIB. J Cyst Fibros 2004; 3:165-72. [PMID: 15463903 DOI: 10.1016/j.jcf.2004.04.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2003] [Accepted: 04/21/2004] [Indexed: 11/16/2022]
Abstract
Clinical and environmental strains of Burkholderia cenocepacia belonging to the recA lineages IIIA and IIIB were examined for exopolysaccharide (EPS) production. The exopolysaccharides structure was determined using mainly gas chromatography coupled to mass spectrometry and NMR spectroscopy. All the strains produced Cepacian, a highly branched polysaccharide constituted of a heptasaccharide repeating unit, composed of one rhamnose, one glucose, one glucuronic acid, one mannose and three galactose residues. This polymer is the most common exopolysaccharide produced by strains of the Burkholderia cepacia (Bcc) complex. One clinical strain produced also another polysaccharide constituted of three galactose units and one 3-deoxy-D-manno-2-octulosonic acid residues, a polymer that was previously isolated from two strains of B. cepacia genomovar I and B. cenocepacia IIIA.
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Affiliation(s)
- Luigi Chiarini
- Unità Biotecnologie, C.R. Casaccia, ENEA, 00060 Rome, Italy
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Manno G, Dalmastri C, Tabacchioni S, Vandamme P, Lorini R, Minicucci L, Romano L, Giannattasio A, Chiarini L, Bevivino A. Epidemiology and clinical course of Burkholderia cepacia complex infections, particularly those caused by different Burkholderia cenocepacia strains, among patients attending an Italian Cystic Fibrosis Center. J Clin Microbiol 2004; 42:1491-7. [PMID: 15070994 PMCID: PMC387599 DOI: 10.1128/jcm.42.4.1491-1497.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [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: 11/20/2022] Open
Abstract
In this study, the epidemiology of Burkholderia cepacia complex (Bcc) recovered from the sputum of 75 patients attending the Genoa Cystic Fibrosis (CF) Center at the Gaslini Children's Hospital (Genoa, Italy) was investigated, and the clinical course of the CF patients infected with the different species and genomovars of Bcc was evaluated. All isolates were analyzed for genomovar status by recA gene polymorphism and subsequently random amplified polymorphic DNA fingerprinting. Burkholderia cenocepacia is the predominant species recovered from the CF patients infected with Bcc at the Genoa CF Center. Of the other eight species comprising the Bcc, only a few isolates belonging to B. cepacia genomovar I, Burkholderia stabilis, and Burkholderia pyrrocinia were found. Of the four recA lineages of B. cenocepacia, most patients were infected by epidemic strains belonging to lineages IIIA and IIID, whereas only a few patients harbored IIIB strains. Patient-to-patient spread of Bcc among CF patients was mostly associated with B. cenocepacia, in particular with strains belonging to recA lineages IIIA and IIID. The mortality of CF patients infected with Bcc at the Genoa CF Center was significantly higher than mortality among CF patients not infected with Bcc. All of the deaths were associated with the presence of B. cenocepacia, except the case of a patient infected with B. cepacia genomovar I. Within B. cenocepacia, infection with epidemic strains belonging to lineages IIIA and IIID was associated with higher rates of mortality than was infection with lineage IIIB strains. No significant differences in lung function, body weight, and mortality rate were observed between patients infected with epidemic strains belonging to either B. cenocepacia IIIA or B. cenocepacia IIID.
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Affiliation(s)
- Graziana Manno
- Infectious Diseases Research and Diagnosis Laboratory, Italy
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Manno G, Dalmastri C, Tabacchioni S, Lorini R, Minicucci L, Romano L, Giannatasio A, Chiarini L, Bevivino A. BURKHOLDERIA CEPACIA COMPLEX IN UN CENTRO FIBROSI CISTICA ITALIANO: EPIDEMIOLOGIA E DECORSO CLINICO NEI PAZIENTI INFETTATI CON DIFFERENTI RECA LINEAGES DI BURKHOLDERIA CENOCEPACIA. Microbiol Med 2003. [DOI: 10.4081/mm.2003.4224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Ciccillo F, Fiore A, Bevivino A, Dalmastri C, Tabacchioni S, Chiarini L. Effects of two different application methods of Burkholderia ambifaria MCI 7 on plant growth and rhizospheric bacterial diversity. Environ Microbiol 2002; 4:238-45. [PMID: 12010130 DOI: 10.1046/j.1462-2920.2002.00291.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [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: 11/20/2022]
Abstract
In order to acquire a better understanding of the effects of the different delivery modes of bacterial inoculants on plant growth and on the community structure of rhizosphere bacterial populations, Burkholderia ambifaria MCI 7 (formerly B. cepacia MCI 7) was inoculated into the rhizosphere of maize plants by either seed adhesion or incorporation into soil. Plant growth was evaluated at different inoculum concentrations. The community structure of rhizosphere bacterial populations was evaluated by analysing the restriction patterns of the DNA coding for 16S rRNA amplified by polymerase chain reaction (PCR) (ARDRA) of 745 bacterial isolates. A number of diversity indices (richness, Shannon diversity, evenness and mean genetic distance) were calculated for each bacterial population isolated from control and treated plants according to the concept of the r/K strategy. Moreover, the analysis of molecular variance (AMOVA) method was applied to estimate the genetic differences among the various bacterial populations. Our results showed that the method of application can be an essential element in determining the effects of the inoculant on plant growth. In fact, when applied as a maize seed treatment, B. ambifaria MCI 7 promoted plant growth significantly; on the contrary, when incorporated into soil, the same strain reduced plant growth markedly. As far as the bacterial community structure is concerned, B. ambifaria MCI 7 affected the indigenous microflora of treated plants according to the application method: seed treatment brought about an abrupt decrease in bacterial diversity, whereas incorporation into soil increased bacterial diversity. Moreover, changes in bacterial diversity were limited to r-strategist bacteria. In conclusion, B. ambifaria MCI 7 can act as both a plant growth-promoting rhizobacterium and a deleterious rhizobacterium depending on the inoculation method.
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Affiliation(s)
- Fabio Ciccillo
- ENEA - C. R. Casaccia, Dip. to Innovazione, Unità Biotecnologie, Via Anguillarese 301, 00060 S. Maria di Galeria, Rome, Italy
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Bevivino A, Dalmastri C, Tabacchioni S, Chiarini L, Belli ML, Piana S, Materazzo A, Vandamme P, Manno G. Burkholderia cepacia complex bacteria from clinical and environmental sources in Italy: genomovar status and distribution of traits related to virulence and transmissibility. J Clin Microbiol 2002; 40:846-51. [PMID: 11880403 PMCID: PMC120285 DOI: 10.1128/jcm.40.3.846-851.2002] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [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: 11/20/2022] Open
Abstract
Sixty-eight Burkholderia cepacia complex isolates recovered from the sputum of 53 cystic fibrosis patients and 75 isolates collected from the maize rhizosphere were compared to each other to assess their genomovar status as well as some traits related to virulence such as antibiotic susceptibility, proteolytic and hemolytic activities, and transmissibility, in which transmissibility is determined by detection of the esmR and cblA genes. Among the clinical isolates, B. cepacia genomovar III comprised the majority of isolates examined and only a very few isolates were assigned to B. cepacia genomovar I, B. stabilis, and B. pyrrocinia; among the environmental isolates a prevalence of B. cepacia genomovar III and B. ambifaria was observed, whereas few environmental isolates belonging to B. cepacia genomovar I and B. pyrrocinia were found. Antibiotic resistance analysis revealed a certain degree of differentiation between clinical and environmental isolates. Proteolytic activity and onion tissue maceration ability were found to be spread equally among both clinical and environmental isolates, whereas larger percentages of environmental isolates than clinical isolates had hemolytic activity. The esmR gene was found exclusively among isolates belonging to B. cepacia genomovar III, with a marked prevalence in clinical isolates, whereas only one clinical isolate belonging to B. cepacia genomovar III was found to bear the cblA gene. In conclusion, the results of the present study show that the species compositions of the clinical and environmental B. cepacia complex populations examined are quite different and that some of the candidate determinants related to virulence and transmissibility are not confined solely to clinical isolates but are also spread among environmental isolates belonging to different species of the B. cepacia complex.
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Affiliation(s)
- Annamaria Bevivino
- Biotechnology and Agriculture Division, ENEA C.R. Casaccia, 00060 S. Maria di Galeria, Rome, Italy
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Fiore A, Laevens S, Bevivino A, Dalmastri C, Tabacchioni S, Vandamme P, Chiarini L. Burkholderia cepacia complex: distribution of genomovars among isolates from the maize rhizosphere in Italy. Environ Microbiol 2001; 3:137-43. [PMID: 11321544 DOI: 10.1046/j.1462-2920.2001.00175.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [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: 11/20/2022]
Abstract
Burkholderia cepacia is a 'complex' in which seven genomic species or genomovars have so far been identified. It appears that all seven B. cepacia genomovars are capable of causing infections in vulnerable persons; in particular, the importance of Burkholderia multivorans (genomovar II) and B. cepacia genomovar III among cystic fibrosis isolates, especially epidemic ones, has been emphasized. In order to acquire a better comprehension of the genomovar composition of environmental populations of B. cepacia, 120 strains were isolated from the rhizosphere of maize plants cultivated in fields located in northern, central and southern Italy. The identification of the different genomovars was accomplished by a combination of molecular polymerase chain reaction (PCR)-based techniques, such as restriction fragment length polymorphism (RFLP) analysis of 16S rDNA (ARDRA), genomovar-specific PCR tests and RFLP analyses based on polymorphisms in the recA gene whole-cell protein electrophoresis. ARDRA analysis allowed us to distinguish between all B. cepacia genomovars except B. cepacia genomovar I, B. cepacia genomovar III and Burkholderia ambifaria (genomovar VII). The latter genomovars were differentiated by means of recA PCR tests and RFLP analyses. Among the rhizospheric isolates of B. cepacia, we found only B. cepacia genomovar I, B. cepacia genomovar III, Burkholderia vietnamiensis (genomovar V) and B. ambifaria. B. cepacia genomovars I and III and B. ambifaria were recovered from all three fields, whereas B. vietnamiensis was detected only in the population isolated from the field located in central Italy. Among strains isolated from northern and southern Italy, the most abundant genomovars were B. ambifaria and B. cepacia genomovar III respectively; in contrast, the population isolated in central Italy showed an even distribution of strains among genomovars. These results indicate that it is not possible to differentiate clinical and environmental strains, or pathogenic and non-pathogenic strains, of the B. cepacia complex simply on the basis of genomovar status, and that the environment may serve as a reservoir for B. cepacia genomovar III infections in vulnerable humans.
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Affiliation(s)
- A Fiore
- Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente, CR Casaccia, Dip. to Innovazione, Rome, Italy
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Tabacchioni S, Chiarini L, Bevivino A, Cantale C, Dalmastri C. Bias Caused by Using Different Isolation Media for Assessing the Genetic Diversity of a Natural Microbial Population. Microb Ecol 2000; 40:169-176. [PMID: 11080375 DOI: 10.1007/s002480000015] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The influence of isolation medium on the biodiversity of Burkholderia cepacia strains recovered from the rhizosphere of Zea mays was evaluated by comparing the genetic diversity of isolates obtained by plating serial dilutions of root macerates on the two selective media TB-T and PCAT. From each medium, 50 randomly chosen colonies were isolated. On the basis of the restriction patterns of DNA coding for 16S rRNA (16S rDNA) amplified by means of PCR (ARDRA), all strains isolated from TB-T medium were assigned to the B. cepacia species, whereas among PCAT isolates only 74% were assigned to the B. cepacia species. Genetic diversity among the PCAT and TB-T isolates was evaluated by the random amplified polymorphic DNA (RAPD) technique. The analysis of molecular variance (AMOVA) method was applied to determine the variance component for RAPD patterns. Most of the genetic diversity (90.59%) was found within the two groups of isolates, but an appreciable amount (9.41%) still separated the two groups (P < 0.001). Mean genetic distances among PCAT isolates (10.39) and TB-T isolates (9.36) were significantly different (P < 0.0001). The results indicate that the two different isolation media select for B. cepacia populations with a different degree of genetic diversity. Moreover, a higher degree of genetic diversity was observed among strains isolated from PCAT medium than among those isolated from TB-T medium.
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Affiliation(s)
- S Tabacchioni
- Dipartimento Innovazione, Divisione Biotecnologie e Agricoltura, ENEA (Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente) C.R. Casaccia, 00060 Rome, Italy
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41
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Chiarini L, Giovannelli V, Bevivino A, Dalmastri C, Tabacchioni S. Different portions of the maize root system host Burkholderia cepacia populations with different degrees of genetic polymorphism. Environ Microbiol 2000; 2:111-8. [PMID: 11243257 DOI: 10.1046/j.1462-2920.2000.00083.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [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: 11/20/2022]
Abstract
In order to acquire a better understanding of the spatial and temporal variations of genetic diversity of Burkholderia cepacia populations in the rhizosphere of Zea mays, 161 strains were isolated from three portions of the maize root system at different soil depths and at three distinct plant growth stages. The genetic diversity among B. cepacia isolates was analysed by means of the random amplified polymorphic DNA (RAPD) technique. A number of diversity indices (richness, Shannon diversity, evenness and mean genetic distance) were calculated for each bacterial population isolated from the different root system portions. Moreover, the analysis of molecular variance (AMOVA) method was applied to estimate the genetic differences among the various bacterial populations. Our results showed that, in young plants, B. cepacia colonized preferentially the upper part of the root system, whereas in mature plants, B. cepacia was mostly recovered from the terminal part of the root system. This uneven distribution of B. cepacia cells among different root system portions partially reflected marked genetic differences among the B. cepacia populations isolated along maize roots on three distinct sampling occasions. In fact, all the diversity indices calculated indicated that genetic diversity increased during plant development and that the highest diversity values were found in mature maize plants, in particular in the middle and terminal portions of the root system. Moreover, the analysis of RAPD patterns by means of the AMOVA method revealed highly significant divergences in the degree of genetic polymorphism among the various B. cepacia populations.
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Affiliation(s)
- L Chiarini
- ENEA (Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente) C.R. Casaccia, Divisione Biotecnologie ed Agricoltura, Rome, Italy.
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42
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Dalmastri C, Chiarini L, Cantale C, Bevivino A, Tabacchioni S. Soil Type and Maize Cultivar Affect the Genetic Diversity of Maize Root-Associated Burkholderia cepacia Populations. Microb Ecol 1999; 38:273-284. [PMID: 10541789 DOI: 10.1007/s002489900177] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Abstract Burkholderia cepacia populations associated with the Zea mays root system were investigated to assess the influence of soil type, maize cultivar, and root localization on the degree of their genetic diversity. A total of 180 B. cepacia isolates were identified by restriction analysis of the amplified 16S rDNA (ARDRA technique). The genetic diversity among B. cepacia isolates was analyzed by the random amplified polymorphic DNA (RAPD) technique, using the 10-mer primer AP5. The analysis of molecular variance (AMOVA) method was applied to estimate the variance components for the RAPD patterns. The results indicated that, among the factors studied, the soil was clearly the dominant one in affecting the genetic diversity of maize root-associated B. cepacia populations. In fact, the percentage of variation among populations was significantly higher between B. cepacia populations recovered from maize planted in different soils than between B. cepacia populations isolated from different maize cultivars and from distinct root compartments such as rhizoplane and rhizosphere. The analysis of the genetic relationships among B. cepacia isolates resulted in dendrograms showing bacterial populations with frequent recombinations and a nonclonal genetic structure. The dendrograms were also in agreement with the AMOVA results. We were able to group strains obtained from distinct soils on the basis of their origin, confirming that soil type had the major effect on the degree of genetic diversity of the maize root-associated B. cepacia populations analyzed. On the other hand, strains isolated from distinct root compartments exhibited a random distribution which confirmed that the rhizosphere and rhizoplane populations analyzed did not significantly differ in their genetic structure.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p273.html</hea
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Affiliation(s)
- C Dalmastri
- ENEA (Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente) C.R. Casaccia, Dipartimento Innovazione, 00060 Rome, Italy
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Bevivino A, Sarrocco S, Dalmastri C, Tabacchioni S, Cantale C, Chiarini L. Characterization of a free-living maize-rhizosphere population of Burkholderia cepacia: effect of seed treatment on disease suppression and growth promotion of maize. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00539.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Di Cello F, Bevivino A, Chiarini L, Fani R, Paffetti D, Tabacchioni S, Dalmastri C. Biodiversity of a Burkholderia cepacia population isolated from the maize rhizosphere at different plant growth stages. Appl Environ Microbiol 1997; 63:4485-93. [PMID: 9361434 PMCID: PMC168767 DOI: 10.1128/aem.63.11.4485-4493.1997] [Citation(s) in RCA: 148] [Impact Index Per Article: 5.5] [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: 02/05/2023] Open
Abstract
A Burkholderia cepacia population naturally occurring in the rhizosphere of Zea mays was investigated in order to assess the degree of root association and microbial biodiversity at five stages of plant growth. The bacterial strains isolated on semiselective PCAT medium were mostly assigned to the species B. cepacia by an analysis of the restriction patterns produced by amplified DNA coding for 16S rRNA (16S rDNA) (ARDRA) with the enzyme AluI. Partial 16S rDNA nucleotide sequences of some randomly chosen isolates confirmed the ARDRA results. Throughout the study, B. cepacia was strictly associated with maize roots, ranging from 0.6 to 3.6% of the total cultivable microflora. Biodiversity among 83 B. cepacia isolates was analyzed by the random amplified polymorphic DNA (RAPD) technique with two 10-mer primers. An analysis of RAPD patterns by the analysis of molecular variance method revealed a high level of intraspecific genetic diversity in this B. cepacia population. Moreover, the genetic diversity was related to divergences among maize root samplings, with microbial genetic variability markedly higher in the first stages of plant growth; in other words, the biodiversity of this rhizosphere bacterial population decreased over time.
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Affiliation(s)
- F Di Cello
- Dipartimento Innovazione, ENEA (Ente Nazionale per le Nuove Tecnologie, l'Energia e l'Ambiente) C. R. Casaccia, Rome, Italy
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Borello U, Aracri B, Dalmastri C, Farini D, Ponti D, Giuliano G. Transcriptional Regulation of Nuclear Genes Controlling Plastid Differentiation in Tomato. BIOTECHNOL BIOTEC EQ 1993. [DOI: 10.1080/13102818.1993.10818694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Visca P, Dalmastri C, Verzili D, Antonini G, Chiancone E, Valenti P. Interaction of lactoferrin with Escherichia coli cells and correlation with antibacterial activity. Med Microbiol Immunol 1990; 179:323-33. [PMID: 2093835 DOI: 10.1007/bf00189610] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [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: 12/30/2022]
Abstract
It has been established that the antimicrobial activity of lactoferrin towards Escherichia coli is enhanced by a direct contact between the protein and the microbial cell and that, in the case of E. coli K-12 strains, an antibacterial activity of lactoferrin unrelated to iron withdrawal is present. Evidence is now reported that lactoferrin binds to surface structures expressed in E. coli K-12 strains grown in either an "excess" or "stress" of iron. Under the experimental conditions used, lactoferrin binding both in the apo and in the iron-saturated form yields a maximum of 1.6 X 10(5) bound molecules/E. coli K-12 cell; the amount of lactoferrin bound does not depend on the expression of the iron-regulated outer membrane proteins. In contrast, lactoferrin does not bind to E. coli clinical isolates. Apo-lactoferrin (at 500 micrograms/ml in a chemically defined medium) inhibits the growth of E. coli K-12 strains but not of clinical isolates. These findings suggest that the antibacterial activity of the protein could be associated to its binding to the cell surface.
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Affiliation(s)
- P Visca
- Istituto di Microbiologia, Facoltà di Medicina e Chirurgia, Roma, Italy
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47
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Visca P, Berlutti F, Vittorioso P, Dalmastri C, Thaller MC, Valenti P. Growth and adsorption of Streptococcus mutans 6715-13 to hydroxyapatite in the presence of lactoferrin. Med Microbiol Immunol 1989; 178:69-79. [PMID: 2733635 DOI: 10.1007/bf00203302] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [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: 01/02/2023]
Abstract
The growth of Streptococcus mutans 6715-13 in a rich medium (Todd Hewitt broth) was drastically reduced by addition of apo-lactoferrin (apo-Lf); this effect was bacteriostatic and reversible by saturation of Lf with iron. The influence of Lf, salivary proteins (SP) and bovine serum albumin (BSA) on the attachment of Streptococcus mutans to hydroxyapatite (HA) was successively investigated. Sorption of Lf, SP, and BSA to HA was dependent on the protein concentration and reached the end-point at about 80 mg of proteins per gram of HA. Similarly, the number of streptococci adsorbed to HA was correlated to the amount of cells available up to at least 10(7) cells per mg of HA. The adsorption of Lf, SP and BSA on HA reduced the number of attaching S. mutans cells. In particular, SP reduced the adsorption of S. mutans by 30%, whereas pre-coating of HA with apo- or iron-saturated Lf resulted in a three orders of magnitude reduction of S. mutans adsorption to HA, as demonstrated by means of different experimental procedures. The powerful adherence-inhibiting effect of apo-Lf together with its noticeable antibacterial activity towards S. mutans points to a biological significance of these phenomena also in vivo.
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Affiliation(s)
- P Visca
- Istituto di Microbiologia, Facoltà di Medicina e Chirurgia, Università La Sapienza, Roma, Italy
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Dalmastri C, Valenti P, Visca P, Vittorioso P, Orsi N. Enhanced antimicrobial activity of lactoferrin by binding to the bacterial surface. Microbiologica 1988; 11:225-30. [PMID: 2971856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In order to elucidate the mechanisms involved in the antibacterial activity of lactoferrin, quantitative determinations of siderophore production and lactoferrin adsorption on various bacterial species were performed. The binding of lactoferrin took place both on Gram-positive and Gram-negative species and occurred with bacterial cells grown in stress or in excess of iron. The different degrees of sensitivity to lactoferrin observed could not be directly related to the type and amount of siderophores produced. However, it was possible to find a correlation between the capacity of some strains to bind lactoferrin and their sensitivity to this protein. These data suggest that the binding of lactoferrin on the cell surface can result in an antibacterial activity additional to iron witholding.
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Affiliation(s)
- C Dalmastri
- Istituto di Microbiologia, Università di Roma La Sapienza, Italy
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