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Lo Presti A, Di Martino A, Ambrosio L, De Sabato L, Knijn A, Vaccari G, Di Bartolo I, Morabito S, Terregino C, Fusaro A, Monne I, Giussani E, Tramuto F, Maida CM, Mazzucco W, Costantino C, Rueca M, Giombini E, Gruber CEM, Capobianchi MR, Palamara AT, Stefanelli P. Tracking the Selective Pressure Profile and Gene Flow of SARS-CoV-2 Delta Variant in Italy from April to October 2021 and Frequencies of Key Mutations from Three Representative Italian Regions. Microorganisms 2023; 11:2644. [PMID: 38004656 PMCID: PMC10673055 DOI: 10.3390/microorganisms11112644] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions. The selective pressure and the frequency of amino acid substitutions and the prediction of their possible impact on the stability of the proteins were investigated. Delta variant dataset, in this study, identified 68 sites under positive selection: 16 in the spike (23.5%), 11 in nsp2 (16.2%) and 10 in nsp12 (14.7%) genes. Three of the positive sites in the spike were located in the receptor-binding domain (RBD). In Delta genomes from the three regions, 6 changes were identified as very common (>83.7%), 4 as common (>64.0%), 21 at low frequency (2.1%-25.0%) and 29 rare (≤2.0%). The detection of positive selection on key mutations may represent a model to identify recurrent signature mutations of the virus.
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Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luigina Ambrosio
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luca De Sabato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Gabriele Vaccari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Calogero Terregino
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Alice Fusaro
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Isabella Monne
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Edoardo Giussani
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Fabio Tramuto
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Carmelo Massimo Maida
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Walter Mazzucco
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Claudio Costantino
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
- Saint Camillus International University of Health Sciences, Via di Sant’Alessandro, 8, 00131 Rome, Italy
- Department of Infectious Tropical Diseases and Microbiology, Sacro Cuore Don Calabria Hospital I.R.C.C.S., Via Don A. Sempreboni 5, 37024 Negrar di Valpolicella, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
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Knijn A, Michelacci V, Gigliucci F, Tozzoli R, Chiani P, Minelli F, Scavia G, Ventola E, Morabito S. IRIDA-ARIES Genomics, a key player in the One Health surveillance of diseases caused by infectious agents in Italy. Front Public Health 2023; 11:1151568. [PMID: 37361153 PMCID: PMC10289303 DOI: 10.3389/fpubh.2023.1151568] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/12/2023] [Indexed: 06/28/2023] Open
Abstract
Pathogen genomics is transforming surveillance of infectious diseases, deepening our understanding of evolution and diffusion of etiological agents, host-pathogen interactions and antimicrobial resistance. This discipline is playing an important role in the development of One Health Surveillance with public health experts of various disciplines integrating methods applied to pathogen research, monitoring, management and prevention of outbreaks. Especially with the notion that foodborne diseases may not be transmitted by food only, the ARIES Genomics project aimed to deliver an Information System for the collection of genomic and epidemiological data to enable genomics-based surveillance of infectious epidemics, foodborne outbreaks and diseases at the animal-human interface. Keeping in mind that the users of the system comprised persons with expertise in a wide variety of domains, the system was expected to be used with a low learning curve directly by the persons target of the analyses' results, keeping the information exchange chains as short as possible. As a result, the IRIDA-ARIES platform (https://irida.iss.it/) provides an intuitive web-based interface for multisectoral data collection and bioinformatic analyses. In practice, the user creates a sample and uploads the Next-generation sequencing reads, then an analysis pipeline is launched automatically performing a series of typing and clustering operations fueling the information flow. Instances of IRIDA-ARIES host the Italian national surveillance system for infections by Listeria monocytogenes (Lm) and the surveillance system for infections by Shigatoxin-producing Escherichia coli (STEC). As of today, the platform does not provide tools to manage epidemiological investigations but serves as an instrument of aggregation for risk monitoring, capable of triggering alarms on possible critical situations that might go unnoticed otherwise.
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Affiliation(s)
- Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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Montalbano Di Filippo M, Boni A, Chiani P, Marra M, Carollo M, Cristofari L, Minelli F, Knijn A, Morabito S. Exploring the nature of interaction between shiga toxin producing Escherichia coli (STEC) and free-living amoeba - Acanthamoeba sp. Front Cell Infect Microbiol 2022; 12:926127. [PMID: 36159652 PMCID: PMC9504058 DOI: 10.3389/fcimb.2022.926127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Free-living amoebae (FLA) are widely distributed protozoa in nature, known to cause severe eye infections and central nervous system disorders. There is growing attention to the potential role that these protozoa could act as reservoirs of pathogenic bacteria and, consequently, to the possibility that, the persistence and spread of the latter may be facilitated, by exploiting internalization into amoebae. Shiga toxin-producing strains of Escherichia coli (STEC) are zoonotic agents capable of causing serious diseases, such as hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Cattle represent the main natural reservoir of STEC, which are frequently found also in other domestic and wild ruminants, often without causing any evident symptoms of disease. The aspects related to the ecology of STEC strains in animal reservoirs and the environment are poorly known, including the persistence of these microorganisms within niches unfavorable to survival, such as soils or waters. In this study we investigated the interaction between STEC strains of serotype O157: H7 with different virulence gene profiles, and a genus of a wild free-living amoeba, Acanthamoeba sp. Our results confirm the ability of STEC strains to survive up to 20 days within a wild Acanthamoeba sp., in a quiescent state persisting in a non-cultivable form, until they reactivate following some stimulus of an unknown nature. Furthermore, our findings show that during their internalization, the E. coli O157 kept the set of the main virulence genes intact, preserving their pathogenetic potential. These observations suggest that the internalization in free-living amoebae may represent a means for STEC to resist in environments with non-permissive growth conditions. Moreover, by staying within the protozoa, STEC could escape their detection in the vehicles of infections and resist to the treatments used for the disinfection of the livestock environment.
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Affiliation(s)
- Margherita Montalbano Di Filippo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Margherita Montalbano Di Filippo,
| | - Arianna Boni
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Chiani
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Manuela Marra
- Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Carollo
- Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Lucrezia Cristofari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Fabio Minelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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Gigliucci F, van Hoek AHAM, Chiani P, Knijn A, Minelli F, Scavia G, Franz E, Morabito S, Michelacci V. Genomic Characterization of hlyF-positive Shiga Toxin-Producing Escherichia coli, Italy and the Netherlands, 2000-2019. Emerg Infect Dis 2021; 27:853-861. [PMID: 33622476 PMCID: PMC7920663 DOI: 10.3201/eid2703.203110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Shiga toxin–producing Escherichia coli (STEC) O80:H2 has emerged in Europe as a cause of hemolytic uremic syndrome associated with bacteremia. STEC O80:H2 harbors the mosaic plasmid pR444_A, which combines several virulence genes, including hlyF and antimicrobial resistance genes. pR444_A is found in some extraintestinal pathogenic E. coli (ExPEC) strains. We identified and characterized 53 STEC strains with ExPEC-associated virulence genes isolated in Italy and the Netherlands during 2000–2019. The isolates belong to 2 major populations: 1 belongs to sequence type 301 and harbors diverse stx2 subtypes, the intimin variant eae-ξ, and pO157-like and pR444_A plasmids; 1 consists of strains belonging to various sequence types, some of which lack the pO157 plasmid, the locus of enterocyte effacement, and the antimicrobial resistance–encoding region. Our results showed that STEC strains harboring ExPEC-associated virulence genes can include multiple serotypes and that the pR444_A plasmid can be acquired and mobilized by STEC strains.
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Lauzi S, Luzzago C, Chiani P, Michelacci V, Knijn A, Pedrotti L, Corlatti L, Buccheri Pederzoli C, Scavia G, Morabito S, Tozzoli R. Free-ranging red deer (Cervus elaphus) as carriers of potentially zoonotic Shiga toxin-producing Escherichia coli. Transbound Emerg Dis 2021; 69:1902-1911. [PMID: 34080316 PMCID: PMC9540879 DOI: 10.1111/tbed.14178] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/31/2021] [Indexed: 11/26/2022]
Abstract
Shiga toxin‐producing E. coli (STEC) are zoonotic foodborne pathogens of outmost importance and interest has been raised in recent years to define the potential zoonotic role of wildlife in STEC infection. This study aimed to estimate prevalence of STEC in free‐ranging red deer (Cervus elaphus) living in areas with different anthropisation levels and describe the characteristics of strains in order to evaluate the potential risk posed to humans. Two‐hundred one deer faecal samples collected in 2016–2018 from animals of Central Italian Alps were examined by bacteriological analysis and PCR screening of E. coli colonies for stx1, stx2 and eae genes. STEC strains were detected in 40 (19.9%) deer, with significantly higher prevalence in offspring than in yearlings. Whole genome analysis was performed to characterise a subset of 31 STEC strains. The most frequently detected serotype was O146:H28 (n = 10, 32.3%). Virulotyping showed different stx subtypes combinations, with stx2b‐only (n = 15, 48.4%) being the most prevalent. All STEC lacked the eae gene but harbored additional virulence genes, particularly adhesins, toxins and/or other colonisation factors also described in STEC isolated from disease in humans. The most frequently detected genes were astA (n = 22, 71%), subAB (n = 21, 68%), iha (n = 26, 83.9%) and lpfA (n = 24, 77%). Four hybrid STEC/Enterotoxigenic E. coli strains were also identified. According to the most recent paradigm for pathogenicity assessment of STEC issued by the European Food Safety Authority, our results suggest that red deer are carriers of STEC strains that may have zoonotic potential, regardless of the anthropisation levels. Particular attention should be drawn to these findings while handling and preparing game meat. Furthermore, deer may release STEC in the environment, possibly leading to the contamination of soil and water sources.
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Affiliation(s)
- Stefania Lauzi
- Department of Veterinary Medicine, University of Milan, Lodi, Italy
| | - Camilla Luzzago
- Department of Veterinary Medicine, University of Milan, Lodi, Italy
| | - Paola Chiani
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità Rome, Rome, Italy
| | - Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità Rome, Rome, Italy
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità Rome, Rome, Italy
| | | | | | | | - Gaia Scavia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità Rome, Rome, Italy
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità Rome, Rome, Italy
| | - Rosangela Tozzoli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità Rome, Rome, Italy
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Michelacci V, Tozzoli R, Arancia S, D'Angelo A, Boni A, Knijn A, Prosseda G, Greig DR, Jenkins C, Camou T, Sirok A, Navarro A, Schelotto F, Varela G, Morabito S. Tracing Back the Evolutionary Route of Enteroinvasive Escherichia coli (EIEC) and Shigella Through the Example of the Highly Pathogenic O96:H19 EIEC Clone. Front Cell Infect Microbiol 2020; 10:260. [PMID: 32582565 PMCID: PMC7283534 DOI: 10.3389/fcimb.2020.00260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/04/2020] [Indexed: 11/13/2022] Open
Abstract
Enteroinvasive Escherichia coli (EIEC) cause intestinal illness through the same pathogenic mechanism used by Shigella spp. The latter species can be typed through genomic and phenotypic methods used for E. coli and have been proposed for reclassification within E. coli species. Recently the first appearance of a highly pathogenic EIEC O96:H19 was described in Europe as the causative agent of two large outbreaks that occurred in Italy and in the United Kingdom. In contrast to Shigella spp and to the majority of EIEC strains, EIEC O96:H19 fermented lactose, lacked pathoadaptive mutations, and showed good fitness in extracellular environment, similarly to non-pathogenic E. coli, suggesting they have emerged following acquisition of the invasion plasmid by a non-pathogenic E. coli. Here we describe the whole genome comparison of two EIEC O96:H19 strains isolated from severe cases of diarrhea in Uruguay in 2014 with the sequences of EIEC O96:H19 available in the public domain. The phylogenetic comparison grouped all the O96:H19 strains in a single cluster, while reference EIEC strains branched into different clades with Shigella strains occupying apical positions. The comparison of the virulence plasmids showed the presence of a complete conjugation region in at least one O96:H19 EIEC. Reverse Transcriptase Real Time PCR experiments confirmed in this strain the expression of the pilin-encoding gene and conjugation experiments suggested its ability to mobilize an accessory plasmid in a recipient strain. Noteworthy, the tra region was comprised between two reversely oriented IS600 elements, which were also found as remnants in another EIEC O96:H19 plasmid lacking the tra locus. We hypothesize that an IS-mediated recombination mechanism may have caused the loss of the conjugation region commonly observed in EIEC and Shigella virulence plasmids. The results of this study support the hypothesis of EIEC originating from non-pathogenic E. coli through the acquisition of the virulence plasmid via conjugation. Remarkably, this study showed the ability of a circulating EIEC strain to mobilize plasmids through conjugation, suggesting a mechanism for the emergence of novel EIEC clones.
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Affiliation(s)
- Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Rosangela Tozzoli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Silvia Arancia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Alfio D'Angelo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Arianna Boni
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Gianni Prosseda
- Department of Biology and Biotechnology "Charles Darwin", Università Sapienza di Roma, Rome, Italy
| | - David R Greig
- Gastrointestinal Bacteria Reference Unit (GBRU), Public Health England, E. coli, Shigella, Yersinia and Vibrio Reference Service, National Infection Service, London, United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit (GBRU), Public Health England, E. coli, Shigella, Yersinia and Vibrio Reference Service, National Infection Service, London, United Kingdom
| | - Teresa Camou
- Departamento de Laboratorios, Ministerio de Salud Pública, Montevideo, Uruguay
| | - Alfredo Sirok
- Departamento de Laboratorios, Ministerio de Salud Pública, Montevideo, Uruguay
| | - Armando Navarro
- Public Health Department, Medicine Faculty, Universidad Nacional Autónoma de Mexico (UNAM), Mexico City, Mexico
| | - Felipe Schelotto
- Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
| | - Gustavo Varela
- Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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7
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Nicolai N, Biasoni D, Catanzaro MA, Colecchia M, Trama A, Hackl M, Eycken EV, Henau K, Dimitrova N, Sekerija M, Dušek L, Mägi M, Malila N, Leinonen M, Velten M, Troussard X, Bouvier V, Guizard AV, Bouvier AM, Arveux P, Maynadié M, Woronoff AS, Robaszkiewic M, Baldi I, Monnereau A, Tretarre B, Colonna M, Molinié F, Bara S, Schvartz C, Lapôtre-Ledoux B, Grosclaude P, Stabenow R, Luttmann S, Nennecke A, Engel J, Schubert-Fritschle G, Heidrich J, Holleczek B, Jónasson JG, Clough-Gorr K, Comber H, Mazzoleni G, Giacomin A, Sutera Sardo A, Barchielli A, Serraino D, De Angelis R, Mallone S, Tavilla A, Pierannunzio D, Rossi S, Santaquilani M, Knijn A, Pannozzo F, Gennaro V, Benfatto L, Ricci P, Autelitano M, Spagnoli G, Fusco M, Usala M, Vitale F, Michiara M, Tumino R, Mangone L, Falcini F, Ferretti S, Filiberti RA, Marani E, Iannelli A, Sensi F, Piffer S, Gentilini M, Madeddu A, Ziino A, Maspero S, Candela P, Stracci F, Tagliabue G, Rugge M, Trama A, Gatta G, Botta L, Capocaccia R, Pildava S, Smailyte G, Calleja N, Johannesen TB, Rachtan J, Góźdź S, Błaszczyk J, Kępska K, de Lacerda GF, Bento MJ, Miranda A, Diba CS, Almar E, Larrañaga N, de Munain AL, Torrella-Ramos A, Díaz García JM, Marcos-Gragera R, Sanchez MJ, Navarro C, Salmeron D, Moreno-Iribas C, Galceran J, Carulla M, Mousavi M, Bouchardy C, M. Ess S, Bordoni A, Konzelmann I, Rashbass J, Gavin A, Brewster DH, Huws DW, Visser O, Bielska-Lasota M, Primic-Zakelj M, Kunkler I, Benhamou E. Testicular germ-cell tumours and penile squamous cell carcinoma: Appropriate management makes the difference. Eur J Surg Oncol 2019. [DOI: 10.1016/j.ejso.2018.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Imbimbo M, Maury JM, Garassino M, Girard N, Hackl M, Eycken EV, Henau K, Dimitrova N, Sekerija M, Dušek L, Mägi M, Malila N, Leinonen M, Velten M, Troussard X, Bouvier V, Guizard AV, Bouvier AM, Arveux P, Maynadié M, Woronoff AS, Robaszkiewicz M, Baldi I, Monnereau A, Tretarre B, Colonna M, Molinié F, Bara S, Schvartz C, Lapôtre-Ledoux B, Grosclaude P, Stabenow R, Luttmann S, Nennecke A, Engel J, Schubert-Fritschle G, Heidrich J, Holleczek B, Jónasson JG, Clough-Gorr K, Comber H, Mazzoleni G, Giacomin A, Sardo AS, Barchielli A, Serraino D, De Angelis R, Mallone S, Tavilla A, Pierannunzio D, Rossi S, Santaquilani M, Knijn A, Pannozzo F, Gennaro V, Benfatto L, Ricci P, Autelitano M, Spagnoli G, Fusco M, Usala M, Vitale F, Michiara M, Tumino R, Mangone L, Falcini F, Ferretti S, Angela Filiberti R, Marani E, Iannelli A, Sensi F, Piffer S, Gentilini M, Madeddu A, Ziino A, Maspero S, Candela P, Stracci F, Tagliabue G, Rugge M, Trama A, Gatta G, Botta L, Capocaccia R, Pildava S, Smailyte G, Calleja N, Johannesen TB, Rachtan J, Góźdź S, Błaszczyk J, Kępska K, de Lacerda GF, Bento MJ, Miranda A, Diba CS, Almar E, Larrañaga N, de Munain AL, Torrella-Ramos A, Díaz García JM, Marcos-Gragera R, Sanchez MJ, Navarro C, Salmeron D, Moreno-Iribas C, Galceran J, Carulla M, Mousavi M, Bouchardy C, Ess SM, Bordoni A, Konzelmann I, Rashbass J, Gavin A, Brewster DH, Huws DW, Visser O, Bielska-Lasota M, Primic-Zakelj M, Kunkler I, Benhamou E. Mesothelioma and thymic tumors: Treatment challenges in (outside) a network setting. Eur J Surg Oncol 2019; 45:75-80. [DOI: 10.1016/j.ejso.2018.01.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/02/2018] [Accepted: 01/07/2018] [Indexed: 10/18/2022] Open
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9
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Gigliucci F, von Meijenfeldt FAB, Knijn A, Michelacci V, Scavia G, Minelli F, Dutilh BE, Ahmad HM, Raangs GC, Friedrich AW, Rossen JWA, Morabito S. Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients. Front Cell Infect Microbiol 2018; 8:25. [PMID: 29468143 PMCID: PMC5808120 DOI: 10.3389/fcimb.2018.00025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 10/30/2017] [Accepted: 01/18/2018] [Indexed: 11/20/2022] Open
Abstract
The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.
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Affiliation(s)
- Federica Gigliucci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy.,Department of Sciences, University Roma Tre, Rome, Italy
| | | | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Gaia Scavia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Fabio Minelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Hamideh M Ahmad
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Gerwin C Raangs
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
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10
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Minicozzi P, Innos K, Sánchez MJ, Trama A, Walsh PM, Marcos-Gragera R, Dimitrova N, Botta L, Visser O, Rossi S, Tavilla A, Sant M, Hackl M, Zielonke N, Van Eycken E, Henau K, Valerianova Z, Dimitrova N, Sekerija M, Dušek L, Zvolský M, Mägi M, Aareleid T, Malila N, Seppä K, Bouvier A, Faivre J, Bossard N, Uhry Z, Colonna M, Stabenow R, Luttmann S, Eberle A, Brenner H, Nennecke A, Engel J, Schubert-Fritschle G, Heidrich J, Holleczek B, Katalinic A, Clough-Gorr K, Mazzoleni G, Bulatko A, Buzzoni C, Giacomin A, Ferretti S, Barchielli A, Caldarella A, Gatta G, Sant M, Amash H, Amati C, Baili P, Berrino F, Bonfarnuzzo S, Botta L, Capocaccia R, Di Salvo F, Foschi R, Margutti C, Meneghini E, Minicozzi P, Trama A, Serraino D, Maso LD, De Angelis R, Caldora M, Carrani E, Francisci S, Knijn A, Mallone S, Pierannunzio D, Roazzi P, Rossi S, Santaquilani M, Tavilla A, Pannozzo F, Natali M, Filiberti R, Marani E, Autelitano M, Spagnoli G, Cirilli C, Fusco M, Vitale M, Traina A, Staiti R, Vitale F, Cusimano R, Michiara M, Tumino R, Falcini F, Caiazzo A, Maspero S, Fanetti A, Zanetti R, Rosso S, Rugge M, Tognazzo S, Pildava S, Smailyte G, Johannesen T, Rachtan J, Góźdź S, Mężyk R, Błaszczyk J, Kępska K, Bielska-Lasota M, Forjaz de Lacerda G, Bento M, Antunes L, Miranda A, Mayer-da-Silva A, Safaei Diba C, Primic-Zakelj M, Almar E, Mateos A, Lopez de Munain A, Larrañaga N, Torrella-Ramos A, Díaz García J, Jimenez-Chillaron R, Marcos-Gragera R, Vilardell L, Moreno-Iribas C, Ardanaz E, Lambe M, Mousavi M, Bouchardy C, Usel M, Ess S, Frick H, Lorez M, Ess S, Herrmann C, Bordoni A, Spitale A, Konzelmann I, Visser O, Damhuis R, Otter R, Coleman M, Allemani C, Rachet B, Rashbass J, Broggio J, Verne J, Gavin A, Fitzpatrick D, Huws D, White C. Quality analysis of population-based information on cancer stage at diagnosis across Europe, with presentation of stage-specific cancer survival estimates: A EUROCARE-5 study. Eur J Cancer 2017; 84:335-353. [DOI: 10.1016/j.ejca.2017.07.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/04/2017] [Accepted: 07/11/2017] [Indexed: 11/28/2022]
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Michelacci V, Orsini M, Knijn A, Delannoy S, Fach P, Caprioli A, Morabito S. Development of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC). Front Microbiol 2016; 7:202. [PMID: 26941726 PMCID: PMC4763077 DOI: 10.3389/fmicb.2016.00202] [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: 11/26/2015] [Accepted: 02/05/2016] [Indexed: 11/13/2022] Open
Abstract
Shiga-toxin producing Escherichia coli (STEC) strains possess a large accessory genome composed of virulence genes existing in multiple allelic variants, which sometimes segregate with specific STEC subpopulations. We analyzed the allelic variability of 91 virulence genes of STEC by Real Time PCR followed by melting curves analysis in 713 E. coli strains including 358 STEC. The 91 genes investigated were located on the locus of enterocyte effacement (LEE), OI-57, and OI-122 pathogenicity islands and displayed a total of 476 alleles in the study population. The combinations of the 91 alleles of each strain were termed allelic signatures and used to perform cluster analyses. We termed such an approach High Resolution Virulence Allelic Profiling (HReVAP) and used it to investigate the phylogeny of STEC of multiple serogroups. The dendrograms obtained identified groups of STEC segregating approximately with the serogroups and allowed the identification of subpopulations within the single groups. The study of the allelic signatures provided further evidence of the coevolution of the LEE and OI-122, reflecting the occurrence of their acquisition through a single event. The HReVAP analysis represents a sensitive tool for studying the evolution of LEE-positive STEC.
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Affiliation(s)
- Valeria Michelacci
- European Reference Laboratory for Escherichia coli, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità Rome, Italy
| | - Massimiliano Orsini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale Teramo, Italy
| | - Arnold Knijn
- Servizio Informatico, Documentazione, Biblioteca e Attività Editoriali, Istituto Superiore di Sanità Rome, Italy
| | - Sabine Delannoy
- Platform IdentyPath, Food Safety Laboratory, ANSES, Université Paris-Est Maisons-Alfort, France
| | - Patrick Fach
- Platform IdentyPath, Food Safety Laboratory, ANSES, Université Paris-Est Maisons-Alfort, France
| | - Alfredo Caprioli
- European Reference Laboratory for Escherichia coli, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità Rome, Italy
| | - Stefano Morabito
- European Reference Laboratory for Escherichia coli, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità Rome, Italy
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Sant M, Allemani C, Santaquilani M, Knijn A, Marchesi F, Capocaccia R. EUROCARE-4. Survival of cancer patients diagnosed in 1995-1999. Results and commentary. Eur J Cancer 2009; 45:931-91. [PMID: 19171476 DOI: 10.1016/j.ejca.2008.11.018] [Citation(s) in RCA: 608] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 11/11/2008] [Accepted: 11/12/2008] [Indexed: 01/09/2023]
Abstract
EUROCARE-4 analysed about three million adult cancer cases from 82 cancer registries in 23 European countries, diagnosed in 1995-1999 and followed to December 2003. For each cancer site, the mean European area-weighted observed and relative survival at 1-, 3-, and 5-years by age and sex are presented. Country-specific 1- and 5-year relative survival is also shown, together with 5-year relative survival conditional to surviving 1-year. Within-country variation in survival is analysed for selected cancers. Survival for most solid cancers, whose prognosis depends largely on stage at diagnosis (breast, colorectum, stomach, skin melanoma), was highest in Finland, Sweden, Norway and Iceland, lower in the UK and Denmark, and lowest in the Czech Republic, Poland and Slovenia. France, Switzerland and Italy generally had high survival, slightly below that in the northern countries. There were between-region differences in the survival for haematologic malignancies, possibly due to differences in the availability of effective treatments. Survival of elderly patients was low probably due to advanced stage at diagnosis, comorbidities, difficult access or lack of availability of appropriate care. For all cancers, 5-year survival conditional to surviving 1-year was higher and varied less with region, than the overall relative survival.
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Affiliation(s)
- Milena Sant
- Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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13
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Ferretti A, Knijn A, Raggi C, Sargiacomo M. High-resolution proton NMR measures mobile lipids associated with Triton-resistant membrane domains in haematopoietic K562 cells lacking or expressing caveolin-1. Eur Biophys J 2003; 32:83-95. [PMID: 12734696 DOI: 10.1007/s00249-002-0273-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2002] [Revised: 11/06/2002] [Accepted: 11/20/2002] [Indexed: 10/25/2022]
Abstract
High-resolution proton NMR spectra of intact tumour cells generally exhibit intense signals due to isotropically mobile lipids (MLs) of still uncertain nature and origin. NMR studies performed on intact wild-type and caveolin-1-infected haematopoietic K562 cells showed that, under our experimental conditions, part of the ML signals are due to lipid complexes resistant to extraction in Triton X-100 at 4 degrees C. This evidence suggests that a portion of NMR-visible lipid structures are compatible with Triton-resistant membrane rafts and therefore biophysically distinct from NMR-visible Triton-soluble lipid bodies. Similarly to lipid rafts and caveolae, the organization of the Triton-insoluble ML domains could be compromised by treatment with beta-octylglucoside or methyl-beta-cyclodextrin. Exposure to exogenous sphingomyelinase caused an increase in ML NMR visibility, indicating the possible involvement of ceramides in ML formation. The mobility of these lipids was found to be temperature sensitive, suggesting a transition in cells going from 4 degrees C to 25-37 degrees C. These new results are here discussed in the light of possible contributions of plasma membrane microdomains to NMR-visible ML signals.
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Affiliation(s)
- A Ferretti
- Laboratory of Cell Biology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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14
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Ferretti A, D'Ascenzo S, Knijn A, Iorio E, Dolo V, Pavan A, Podo F. Detection of polyol accumulation in a new ovarian carcinoma cell line, CABA I: a(1)H NMR study. Br J Cancer 2002; 86:1180-7. [PMID: 11953869 PMCID: PMC2364195 DOI: 10.1038/sj.bjc.6600189] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2001] [Revised: 01/07/2002] [Accepted: 01/10/2002] [Indexed: 12/19/2022] Open
Abstract
Ovarian carcinomas represent a major form of gynaecological malignancies, whose treatment consists mainly of surgery and chemotherapy. Besides the difficulty of prognosis, therapy of ovarian carcinomas has reached scarce improvement, as a consequence of lack of efficacy and development of drug-resistance. The need of different biochemical and functional parameters has grown, in order to obtain a larger view on processes of biological and clinical significance. In this paper we report novel metabolic features detected in a series of different human ovary carcinoma lines, by (1)H NMR spectroscopy of intact cells and their extracts. Most importantly, a new ovarian adenocarcinoma line CABA I, showed strong signals in the spectral region between 3.5 and 4.0 p.p.m., assigned for the first time to the polyol sorbitol (39+/-11 nmol/10(6) cells). (13)C NMR analyses of these cells incubated with [1-(13)C]-D-glucose demonstrated labelled-sorbitol formation. The other ovarian carcinoma cell lines (OVCAR-3, IGROV 1, SK-OV-3 and OVCA432), showed, in the same spectral region, intense resonances from other metabolites: glutathione (up to 30 nmol/10(6) cells) and myo-inositol (up to 50 nmol/10(6) cells). Biochemical and biological functions are suggested for these compounds in human ovarian carcinoma cells, especially in relation to their possible role in cell detoxification mechanisms during tumour progression.
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Affiliation(s)
- A Ferretti
- Laboratory of Cell Biology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
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15
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Casieri C, Knijn A, Podo F, De Luca F. 1H NMR detection of 13C–1H bonds by double 13C editing: application to the discrimination of glucose metabolites. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)00258-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Di Vito M, Lenti L, Knijn A, Iorio E, D'Agostino F, Molinari A, Calcabrini A, Stringaro A, Meschini S, Arancia G, Bozzi A, Strom R, Podo F. 1H NMR-visible mobile lipid domains correlate with cytoplasmic lipid bodies in apoptotic T-lymphoblastoid cells. Biochim Biophys Acta 2001; 1530:47-66. [PMID: 11341958 DOI: 10.1016/s1388-1981(00)00165-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The presence of nuclear magnetic resonance (NMR)-visible mobile lipid (ML) domains in apoptotic lymphoblasts suggests alterations in neutral lipid metabolism and compartmentation during programmed cell death. The detection of similar ML signals in activated lymphocytes raises questions about common mechanisms of ML formation during apoptosis and upon lymphoblast stimulation. Structure and subcellular localization of ML domains were therefore investigated by NMR, fluorescence and electron microscopy in Jurkat T-lymphoblasts either induced to apoptosis (by anthracyclines or dexamethasone or by serum deprivation) or activated by phorbol myristate acetate (PMA) plus ionomycin. ML contents in drug-treated cells correlated linearly with apoptosis, irrespective of the specific inducer and cell cycle arrest phase (r = 0.993, P < 0.001). Similar ML levels were measured in drug-induced apoptotic cells (A approximately 30-40%) and in non-apoptotic PMA/ionomycin-treated lymphoblasts (72 h). Lower ML contents were instead formed in serum-deprived apoptotic cells, with respect to controls. Increases in ML signals were associated, in either apoptotic or activated cells, with the accumulation of cytoplasmic, osmophilic lipid bodies (diameter < or = 1.0 microm), surrounded by own membrane, possessing intramembrane particles. The results support the hypothesis that ML are formed in the cytoplasm of drug-induced apoptotic cells during an early, 'biochemically active' phase of programmed cell death.
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Affiliation(s)
- M Di Vito
- Laboratory of Cell Biology, Istituto Superiore di Sanità, Rome, Italy
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17
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Abstract
The C6 methylene protons were selectively detected in (1)H-NMR spectra of intact glioma cells incubated with 6-(13)C-D-2-deoxyglucose (6-(13)C-2dG), a (13)C-enriched glucose analog that is suitable for monitoring glucose utilization in brain tumors. Spectral editing via (1)H-(13)C scalar coupling was performed with twin spin-echo double resonance (T-SEDOR), a pulse sequence which combines chemical specificity and high sensitivity, requires no solvent pre-saturation, and can easily be adapted to imaging protocols. This work demonstrates the suitability of the pulse sequence for monitoring 6-(13)C-2dG uptake in living cells in vitro, in spite of line-broadening and the occurrence of other strong signals in the spectral region of interest (3.5-4.4 ppm).
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Affiliation(s)
- A Knijn
- Laboratory of Cell Biology, Istituto Superiore di Sanità, 00161 Rome, Italy
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18
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Ferretti A, Knijn A, Iorio E, Pulciani S, Giambenedetti M, Molinari A, Meschini S, Stringaro A, Calcabrini A, Freitas I, Strom R, Arancia G, Podo F. Biophysical and structural characterization of 1H-NMR-detectable mobile lipid domains in NIH-3T3 fibroblasts. Biochim Biophys Acta 1999; 1438:329-48. [PMID: 10366776 DOI: 10.1016/s1388-1981(99)00071-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Nature and subcellular localization of 1H-NMR-detectable mobile lipid domains (ML) were investigated by NMR, Nile red fluorescence and electron microscopy, in NIH-3T3 fibroblasts and their H-ras transformants (3T3ras) transfected with a high number of oncogene copies. Substantial ML levels (ratio of (CH2)n/CH3 peak areas R=1. 56+/-0.33) were associated in untransformed fibroblasts with both (a) intramembrane amorphous lipid vesicles, about 60 nm in diameter, distinct from caveolae; and (b) cytoplasmic, osmiophilic lipid bodies surrounded by own membrane, endowed of intramembrane particles. 2D NMR maps demonstrated that ML comprised both mono- and polyunsaturated fatty chains. Lower ML signals were detected in 3T3ras (R=0.76+/-0.37), under various conditions of cell growth. Very few (if any) lipid bodies and vesicles were detected in the cytoplasmic or membrane compartments of 3T3ras cells with R<0.4, while only intramembrane lipid vesicles were associated with moderate R values. Involvement of phosphatidylcholine hydrolysis in ML generation was demonstrated by selective inhibition of endogenous phospholipase C (PC-plc) or by exposure to bacterial PC-plc. This study indicates that: (1) both cytoplasmic lipid bodies and membrane vesicles (possibly in mutual dynamic exchange) may contribute (although to a different extent) to ML signals; and (2) high levels of ras-transfection either inhibit ML formation or facilitate their extrusion from the cell.
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Affiliation(s)
- A Ferretti
- Laboratory of Cell Biology, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
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19
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Bovée W, Canese R, Decorps M, Forssell-Aronsson E, Le Fur Y, Howe F, Karlsen O, Knijn A, Kontaxis G, Kügel H, McLean M, Podo F, Slotboom J, Vikhoff B, Ziegler A. Absolute metabolite quantification by in vivo NMR spectroscopy: IV. Multicentre trial on MRSI localisation tests. Magn Reson Imaging 1998; 16:1113-25. [PMID: 9839995 DOI: 10.1016/s0730-725x(98)00120-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [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: 10/18/2022]
Abstract
The difference between the experimental and theoretical spatial response function (SRF) of a narrow tube with water is used for a localization test for magnetic resonance spectroscopic imaging (MRSI). From this difference a quantitative performance parameter is derived for the relative amount of signal within a limited region in the field of view. The total signal loss by the MRSI experiment and eddy currents is described by a parameter SL derived from the signal intensities of two echoes. Results of a European multi-centre trial show that this approach is suited for assessment of MRSI localization performance.
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Affiliation(s)
- W Bovée
- Department of Applied Physics, University of Technology, Delft, The Netherlands.
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20
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De Beer R, Van den Boogaart A, Cady E, Graveron-Demilly D, Knijn A, Langenberger KW, Lindon JC, Ohlhoff A, Serraî H, Wylezinska-Arridge M. Absolute metabolite quantification by in vivo NMR spectroscopy: V. Multicentre quantitative data analysis trial on the overlapping background problem. Magn Reson Imaging 1998; 16:1127-37. [PMID: 9839996 DOI: 10.1016/s0730-725x(98)00121-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [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: 11/16/2022]
Abstract
The goal of this study was to establish the best approach for quantifying nuclear magnetic resonance (NMR) lines, that in the frequency domain are overlapping with broad, unwanted background features. To perform the quantitative data analysis in a controlled way, test signals were designed and utilised, derived from two different real-world in vivo nuclear magnetic resonance signals. One of the main conclusions of the study was that the quantification methods currently available to the biomedical research groups can deliver the correct values of the quantitative parameters, but that great care should be taken in using optimal input parameters for the computer programs concerned.
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Affiliation(s)
- R De Beer
- Department of Applied Physics, University of Technology, Delft, The Netherlands.
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21
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De Beer R, Barbiroli B, Gobbi G, Knijn A, Kügel H, Langenberger KW, Tkác I, Topp S. Absolute metabolite quantification by in vivo NMR spectroscopy: III. Multicentre 1H MRS of the human brain addressed by one and the same data-analysis protocol. Magn Reson Imaging 1998; 16:1107-11. [PMID: 9839994 DOI: 10.1016/s0730-725x(98)00119-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- R De Beer
- Department of Applied Physics, Delft University of Technology, The Netherlands.
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22
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Knijn A, Ferretti A, Zhang PJ, Giambenedetti M, Molinari A, Meschini S, Pulciani S, Podo F. Lower levels of 1H MRS-visible mobile lipids in H-ras transformed tumorigenic fibroblasts with respect to their untransformed parental cells. Cell Mol Biol (Noisy-le-grand) 1997; 43:691-701. [PMID: 9298591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
High resolution 1H MRS studies report increased mobile neutral lipid (MNL) signals in transformed and malignant as well as in some in vitro cultured embryonic cells. Nature, subcellular localization and biological function of MNL are still under debate. This work was aimed at assessing alterations induced in MNL signals of NIH-3T3 mouse embryo fibroblasts by transformation with human HJ-ras oncogene. Lower MRS-visible MNL levels were unexpectedly detected in ras-transformed, in vivo tumorigenic fibroblasts, with respect to their untransformed and non-tumorigenic parental cells. MRS, gas chromatography and chemical analysis on cells and their lipid extracts indicated that these spectral differences could hardly be attributed to different triacylglycerol, free fatty acids and total cholesterol levels or to changes in the fatty acyl degree of unsaturation and average chain length. Additional, possibly more relevant mechanisms of regulation of MNL mobility may implicate the extensive morphogenetic changes and reorganization of cytoskeleton components (notably actin) associated with ras-transformation.
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Affiliation(s)
- A Knijn
- Laboratory of Cell Biology, Istituto Superiore di Sanità, Roma, Italy
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Carapella CM, Carpinelli G, Knijn A, Raus L, Caroli F, Podo F. Potential role of in vitro 1H magnetic resonance spectroscopy in the definition of malignancy grading of human neuroepithelial brain tumours. Acta Neurochir Suppl 1997; 68:127-32. [PMID: 9233428 DOI: 10.1007/978-3-7091-6513-3_24] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The increasing sensitivity of neuro-imaging in the diagnosis of brain expanding lesions is not directly related to biopathological specificity and new technological approaches are under study. In particular Magnetic Resonance Spectroscopy (MRS) allows evaluation of some biochemical pathways whose metabolic alterations may be correlated with the nature and malignancy grading of primary brain tumours. In the present study the author performed an in vitro high field 1H MRS (9.4 and 14.1 T) analysis of specimens obtained from stereotactic biopsy or microsurgical removal of primary brain tumours. Different samples derived from heterogeneous areas and/or infiltrated perilesional regions were examined. This study was principally focused on malignancy grading of gliomas and its correlation with the ratio (R) between the resonance band arising from choline containing compounds (between 3.14 and 3.35 ppm) and the total creatine signal (3.0 ppm). Analyses allowed significant discrimination between astrocytomas (R = 2.4 +/- 0.6) and glioblastoma (GBM) (R = 4.4 +/- 1.3) [p < 0.002]; however the results did not allow discrimination between differentiated and anaplastic astrocytomas. The GBM showed the largest spread of values corresponding to their higher level of tissue heterogeneity and de-differentiation. Studies on non astrocytic brain tumours indicated that even higher R values were exhibited by oligodendrogliomas, even in well differentiated forms (p < 0.02 with respect to GBM). Moreover, preliminary observations indicated that signals arising from other metabolites may also contribute to a differential diagnosis of different oncotypes. Among these glycine appears particularly relevant, since higher levels were measured for this amino acid in GBM with respect to both astrocytomas and oligodendrogliomas.
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Affiliation(s)
- C M Carapella
- Department of Neurosurgery, Istituto Nazionale Tumori Regina Elena, Roma, Italy
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Overloop K, Van Hecke P, Vanstapel F, Chen H, Van Huffel S, Knijn A, van Ormondt D. Evaluation of signal processing methods for the quantification of a multi-exponential signal: the glycogen 13C-1 NMR signal. NMR Biomed 1996; 9:315-321. [PMID: 9134542 DOI: 10.1002/(sici)1099-1492(199610)9:7<315::aid-nbm429>3.0.co;2-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The 13C-1 NMR peak in proton-decoupled spectra of liver glycogen solution was quantitatively analyzed by three types of model-function fitting algorithms: iterative line-fitting in the frequency domain (MDCON); iterative least-squares fitting (VARPRO) in the time domain; and noniterative singular value decomposition-based analysis (HTLS), also in the time domain. Quantification results were compared with manual integration values. Performance of the algorithms was tested at different signal-to-noise ratios (S/N) of the glycogen C-1 peak. This was achieved by varying the number of scans summed prior to analysis. Since T2 relaxation in glycogen has been shown to be multiexponential [Overloop, K. et al. Magn. Reson. Med. 36, 45-51 (1996], the exact quantification of the C-1 glycogen signal requires a model function comprising a sum of Lorentzian components, each with a different broadening at the glycogen frequency. This paper focuses on the performances of the above methods to fit such a multicomponent resonance line. In the frequency domain, line fitting with two Lorentz lines gives good results at sufficiently high S/N. In the time domain, VARPRO performs better than HTLS because fixed values can be imposed to the linewidth of the components at the common C-1 frequency, thereby reducing convergence problems at low S/N.
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Affiliation(s)
- K Overloop
- Biomedical NMR Unit, Faculty of Medicine, Katholieke Universiteit Leuven, Belgium
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Podo F, Ferretti A, Knijn A, Zhang P, Ramoni C, Barletta B, Pini C, Baccarini S, Pulciani S. Detection of phosphatidylcholine-specific phospholipase C in NIH-3T3 fibroblasts and their H-ras transformants: NMR and immunochemical studies. Anticancer Res 1996; 16:1399-412. [PMID: 8694508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Although evidence supports constitutive activation of phosphatidylcholine specific phospholipase C (PC-plc) in rastransformed fibroblasts, no studies have been devoted to measure the basal activity levels of this enzyme, its molecular characteristics and subcellular localization. This paper reports for the first time measurements of the activity of different enzymes responsible for PC hydrolysis (PC-plc; phospholipases A2 (pla2) and A1 (pla1)) in homogenates of murine NIH-3T3 fibroblasts (3T3) and their transformants obtained by human H-ras transfection (3T3ras). To this end, 31P NMR analyses were carried out on total cell homogenates, incubated in the presence of mixed diheptanoylphosphatidylcholine: sphingomyelin (DHPC:SM) unilamellar vesicles (SLUV), in which DHPC acts as a suitable substrate for water-soluble lipolytic enzymes. The basal PC-plc activity levels (0.66 +/- 0.14 and 0.38 +/- 0.10 nmol/10(6) cells.hour in 3T3 and 3T3ras fibroblasts, respectively),were substantially higher (over 30-50x) than those reported in the literature for normal mammalian cells (dog heart myocytes). Moreover the PC-plc activity was about 15-30 times lower than the overall PC deacylation activity in both clones. The use of high titer polyclonal antibodies, raised in a rabbit against bacterial PC-plc, allowed identification of one cross-reactive mammalian PC-plc component (M(r) 66 kD) in cell lysates of both 3T3 and 3T3ras fibroblasts, and detection, by indirect immunofluorescence, of its subcellular localization. In control 3T3 fibroblasts (in the late log-phase of growth) the enzyme was exclusively located in the cytosol, while in H-ras transformed cells it was massively exposed on the external side of the membrane. This new finding strongly suggests that the oncogenic product p2Iras is able to induce (or mediate) translocation of PC-plc across the plasma membrane of ras transformed cells, with possible implications not only on cell biochemistry (enhancement of PC-plc activity, and consequent production of intra- and extracellular PCho and accumulation of neutral lipids) but also on cell-cell interaction mechanisms which facilitate tumour invasion and metastasis of oncogene-transformed cells.
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Affiliation(s)
- F Podo
- Department of Cell Biology, Istituto Superiore di Sanità, Roma, Italy
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