DNA methylation is an important mechanism involved in bacteria limiting foreign DNA acquisition, ... more DNA methylation is an important mechanism involved in bacteria limiting foreign DNA acquisition, maintenance of mobile genetic elements, DNA mismatch repair, and gene expression. Changes in DNA methylation pattern are observed in bacteria under stress conditions, including exposure to antimicrobial compounds. These changes can result in transient and fast-appearing adaptive antibiotic resistance (AdR) phenotypes, e.g., strain overexpressing efflux pumps. DNA methylation can be related to DNA mutation rate, because it is involved in DNA mismatch repair systems and because methylated bases are well-known mutational hotspots. The AdR process can be the first important step in the selection of antibiotic-resistant strains, allowing the survival of the bacterial population until more efficient resistant mutants emerge. Epigenetic modifications can be investigated by third-generation sequencing platforms that allow us to simultaneously detect all the methylated bases along with the DNA se...
Additional file 4 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing
Additional file 4: Table S4. Melting temperature differences among instruments and operators. The... more Additional file 4: Table S4. Melting temperature differences among instruments and operators. The median of the average melting temperatures differences for each strain among instruments and operators are reported. In brackets, minimum and maximum difference values are reported. The comparisons between the two operators on the same instrument are reported in bold.
We describe two multi drug-resistant (MDR) carbapenemase-producing Escherichia coli clinical isol... more We describe two multi drug-resistant (MDR) carbapenemase-producing Escherichia coli clinical isolates from an acute hospital in Milan. Both strains, isolated from a surgical wound sample and a surveillance rectal swab respectively, were positive for a blaNDM-type gene by Xpert Carba-R test. The whole-genome sequence characterization disclosed several resistance determinants: blaNDM-5, blaCMY-42, blaTEM-198, rmtB, mphA. The two isolates belonged to phylogenetic group A, sequence type (ST) 1702 and serotype O89:H9. PCR-based replicon typing and conjugation assay demonstrated an IncI1 plasmid localization for both blaNDM-5 and blaCMY-42 genes. This is the first report of a ST1702 NDM-5 and CMY-42- producing E. coli clone in Italy.
Inflammatory Bowel Diseases (IBDs) are gastrointestinal disorders characterized by chronic, relap... more Inflammatory Bowel Diseases (IBDs) are gastrointestinal disorders characterized by chronic, relapsing inflammation, with growing incidence worldwide over the last decades and distinctive features in the pediatric age. An increasing body of evidence indicates that gut microbiota plays a major role in inflammatory disorders, including IBDs. In this review we will discuss the most recent evidences on dysbiotic changes associated with gut inflammation, as well as environmental and genetic factors contributing to IBD pathogenesis, with a focus on the peculiarities of the pediatric age.
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Obesity in childhood and adolescence is considered the most prevalent nutritional disorder, in wh... more Obesity in childhood and adolescence is considered the most prevalent nutritional disorder, in which eating behaviours represent one important factors of influence. Many aspects influence eating behaviours, but taste is considered the main predictor. However, data concerning correlations of obesity, taste sensitivity and behavioural attitudes, such as food neophobia, in children and adolescents are inconsistent. Moreover, it has been suggested that oral bacteria could have a possible role in obesity development and, also, in taste perception. In this context, the present study focused on host related factors with a proposed link to weight gain. To this purpose, taste sensitivity, salivary microbiota composition and food neophobia were compared between children and adolescents with and without obesity in a cross-sectional study. Results showed that children with obesity presented a significantly lower ability in correctly identifying taste qualities and were characterized by a lesser number of Fungiform Papillae (reported as FP/cm 2) compared to normal-weight subjects. Differences in the ecological indexes of microbial alpha-diversity was found between subjects with obesity and normal-weight ones. Moreover, independently from nutritional status, some bacterial genera seemed to differ between subjects with different sensitivity. The potentiality of this multidisciplinary approach could help to better understand and deepen the sensory-driven and microbiological factors related to weight gain.
Billions of microorganisms, or “microbiota”, inhabit the gut and affect its homeostasis, influenc... more Billions of microorganisms, or “microbiota”, inhabit the gut and affect its homeostasis, influencing, and sometimes causing if altered, a multitude of diseases. The genomes of the microbes that form the gut ecosystem should be summed to the human genome to form the hologenome due to their influence on human physiology; hence the term “microbiome” is commonly used to refer to the genetic make-up and gene–gene interactions of microbes. This review attempts to provide insight into this recently discovered vital organ of the human body, which has yet to be fully explored. We herein discuss the rhythm and shaping of the microbiome at birth and during the first years leading up to adolescence. Furthermore, important issues to consider for conducting a reliable microbiome study including study design, inclusion/exclusion criteria, sample collection, storage, and variability of different sampling methods as well as the basic terminology of molecular approaches, data analysis, and clinical i...
Studies on interleukin-8 receptor expression in ovine neutrophils
18th meeting of the …, 2000
... SFX Query. Items in AIR are protected by copyright, with all rights reserved, unless otherwis... more ... SFX Query. Items in AIR are protected by copyright, with all rights reserved, unless otherwise indicated. Share this record with your favourite social network: Del.icio.us, Citeulike, Connotea, Facebook, Stumble it! reddit, Browser ...
Isolation stress in sheep. Effects on neutrophilic gene expression of CD18-IL-8 and C5a receptors; Stress da isolamento nella pecora. Effetto sull'espressione genica …
Atti della Societa'Italiana …, 2001
... Original title, Stress da isolamento nella pecora. ... ANIMAL DOMESTIQUE, ANIMAL UTILE, BETAI... more ... Original title, Stress da isolamento nella pecora. ... ANIMAL DOMESTIQUE, ANIMAL UTILE, BETAIL, BIOLOGIE, BOVIDAE, CAPRINAE, CATECHOLAMINE, CELLULE, CELLULE SANGUINE, COMPOSE AMINE ... URL: http://www.ismea.it/flex/FixedPages/IT/RicercaStampa.php/L/IT. ...
Additional file 2 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing
Additional file 2: Table S2. Instruments information. For each instrument used in this work, the ... more Additional file 2: Table S2. Instruments information. For each instrument used in this work, the model, the short name (used in manuscript, tables and figure), the sensitivity and the location are reported.
Additional file 3 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing
Additional file 3: Table S3. Strains melting temperatures. The instrument used for the HRM analys... more Additional file 3: Table S3. Strains melting temperatures. The instrument used for the HRM analysis, the operator who performed the HRM analysis, the primer set used, the melting temperature replicates (T1, T2 and T3) and their average melting temperature (aTm) are reported for each strain.
Additional file 1 of MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data
Additional file 1: This file contains a detailed description of the clustering algorithm, of the ... more Additional file 1: This file contains a detailed description of the clustering algorithm, of the input file and of each output file created by the tool.
Cytoskeleton actin changes in IL-2 activated cells
European Journal of Histochemistry, 2009
In the present study we analysed the changes in cytoskeletal actin in lymphoid cells following IL... more In the present study we analysed the changes in cytoskeletal actin in lymphoid cells following IL-2 activation and during cell interactions by means of light and electron microscopy, immunofluorescence and molecular analysis. By morphological analysis we observed a higher fluorescence in the activated cells than in the quiescent ones with no modifications in the cytoskeleton pattern comparing activated to resting cells. The results of molecular analysis indicate that, after IL-2 activation, there is a reorganisation of the actin component of the cell cytoskeleton accompanied by the differential expression of the corresponding genes. A future study will be extended to the analysis of others components of the cytoskeleton network.
Bacterial populations inhabiting a variety of natural and human-associated niches have the abilit... more Bacterial populations inhabiting a variety of natural and human-associated niches have the ability to grow in the form of biofilms. A large part of pathological chronic conditions, and essentially all the bacterial infections associated with implanted medical devices or prosthetics, are caused by microorganisms embedded in a matrix made of polysaccharides, proteins, and nucleic acids. Biofilm infections are generally characterized by a slow onset, mild symptoms, tendency to chronicity, and refractory response to antibiotic therapy. Even though the molecular mechanisms responsible for resistance to antimicrobial agents and host defenses have been deeply clarified, effective means to fight biofilms are still required. Lactic acid bacteria (LAB), used as probiotics, are emerging as powerful weapons to prevent adhesion, biofilm formation, and control overgrowth of pathogens. Hence, using probiotics or their metabolites to quench and interrupt bacterial communication and aggregation, and...
The establishment of gut microbiota is reportedly aberrant in newborns admitted to neonatal inten... more The establishment of gut microbiota is reportedly aberrant in newborns admitted to neonatal intensive care units (NICUs), with detrimental long-term health impacts. Here, we vertically tracked the developing gut bacterial communities of newborns hosted in an NICU during an outbreak sustained by ESBL Klebsiella pneumoniae and compared colonized and noncolonized patients. Most communities were highly variable from one sampling point to the next, and dominated by few taxa, often Proteobacteria and Enterobacteriaceae, with marked interindividual variability. This picture was retrieved independently of colonization status or clinical covariates. Our data support the emerging idea of preterm infants as a population in which no defined microbial signatures are clearly associated to clinical status. Instead, the strong pressure of the nosocomial environment, antibiotics and, in this case, the ongoing outbreak, possibly drive the evolution of microbiota patterns according to individual condi...
Background The rapid identification of pathogen clones is pivotal for effective epidemiological c... more Background The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable for fast and inexpensive pathogen typing protocols. Unfortunately, the mathematical/informatics skills required to analyse HRM data for pathogen typing likely limit the application of this promising technique in hospital settings. Results MeltingPlot is the first tool specifically designed for epidemiological investigations using HRM data, easing the application of HRM typing to large real-time surveillance and rapid outbreak reconstructions. MeltingPlot implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. The tool also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological investigations and it runs in a few seconds even w...
ObjectivesSubspecies pathogen typing is a pivotal tool to detect the emergence of high-risk clone... more ObjectivesSubspecies pathogen typing is a pivotal tool to detect the emergence of high-risk clones in hospital settings and to limit their spreading among patients. Unfortunately, the most used subspecies typing methods (i.e. Pulsed-field Gel Electrophoresis - PFGE, Multi-Locus Sequence Typing - MLST and Whole Genome Sequencing - WGS) are too expensive and time consuming to be suitable for real-time surveillance. Here we present Hypervariable-Locus Melting Typing (HLMT), a novel subspecies typing approach based on High Resolution Melting (HRM) analysis, which allows pathogen typing in a few hours and with ∼5 euros per sample.MethodsHLMT types the strains by clustering them using melting temperatures (HLMT-clustering) and/or by assigning them to Melting Types (MTs) on the basis of a reference dataset (HLMT-assignment). We applied HLMT (clustering and typing) to 134 Klebsiella pneumoniae strains collected during outbreaks or surveillance programs in four hospitals. Then, we compared H...
DNA methylation is an important mechanism involved in bacteria limiting foreign DNA acquisition, ... more DNA methylation is an important mechanism involved in bacteria limiting foreign DNA acquisition, maintenance of mobile genetic elements, DNA mismatch repair, and gene expression. Changes in DNA methylation pattern are observed in bacteria under stress conditions, including exposure to antimicrobial compounds. These changes can result in transient and fast-appearing adaptive antibiotic resistance (AdR) phenotypes, e.g., strain overexpressing efflux pumps. DNA methylation can be related to DNA mutation rate, because it is involved in DNA mismatch repair systems and because methylated bases are well-known mutational hotspots. The AdR process can be the first important step in the selection of antibiotic-resistant strains, allowing the survival of the bacterial population until more efficient resistant mutants emerge. Epigenetic modifications can be investigated by third-generation sequencing platforms that allow us to simultaneously detect all the methylated bases along with the DNA se...
Additional file 4 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing
Additional file 4: Table S4. Melting temperature differences among instruments and operators. The... more Additional file 4: Table S4. Melting temperature differences among instruments and operators. The median of the average melting temperatures differences for each strain among instruments and operators are reported. In brackets, minimum and maximum difference values are reported. The comparisons between the two operators on the same instrument are reported in bold.
We describe two multi drug-resistant (MDR) carbapenemase-producing Escherichia coli clinical isol... more We describe two multi drug-resistant (MDR) carbapenemase-producing Escherichia coli clinical isolates from an acute hospital in Milan. Both strains, isolated from a surgical wound sample and a surveillance rectal swab respectively, were positive for a blaNDM-type gene by Xpert Carba-R test. The whole-genome sequence characterization disclosed several resistance determinants: blaNDM-5, blaCMY-42, blaTEM-198, rmtB, mphA. The two isolates belonged to phylogenetic group A, sequence type (ST) 1702 and serotype O89:H9. PCR-based replicon typing and conjugation assay demonstrated an IncI1 plasmid localization for both blaNDM-5 and blaCMY-42 genes. This is the first report of a ST1702 NDM-5 and CMY-42- producing E. coli clone in Italy.
Inflammatory Bowel Diseases (IBDs) are gastrointestinal disorders characterized by chronic, relap... more Inflammatory Bowel Diseases (IBDs) are gastrointestinal disorders characterized by chronic, relapsing inflammation, with growing incidence worldwide over the last decades and distinctive features in the pediatric age. An increasing body of evidence indicates that gut microbiota plays a major role in inflammatory disorders, including IBDs. In this review we will discuss the most recent evidences on dysbiotic changes associated with gut inflammation, as well as environmental and genetic factors contributing to IBD pathogenesis, with a focus on the peculiarities of the pediatric age.
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Obesity in childhood and adolescence is considered the most prevalent nutritional disorder, in wh... more Obesity in childhood and adolescence is considered the most prevalent nutritional disorder, in which eating behaviours represent one important factors of influence. Many aspects influence eating behaviours, but taste is considered the main predictor. However, data concerning correlations of obesity, taste sensitivity and behavioural attitudes, such as food neophobia, in children and adolescents are inconsistent. Moreover, it has been suggested that oral bacteria could have a possible role in obesity development and, also, in taste perception. In this context, the present study focused on host related factors with a proposed link to weight gain. To this purpose, taste sensitivity, salivary microbiota composition and food neophobia were compared between children and adolescents with and without obesity in a cross-sectional study. Results showed that children with obesity presented a significantly lower ability in correctly identifying taste qualities and were characterized by a lesser number of Fungiform Papillae (reported as FP/cm 2) compared to normal-weight subjects. Differences in the ecological indexes of microbial alpha-diversity was found between subjects with obesity and normal-weight ones. Moreover, independently from nutritional status, some bacterial genera seemed to differ between subjects with different sensitivity. The potentiality of this multidisciplinary approach could help to better understand and deepen the sensory-driven and microbiological factors related to weight gain.
Billions of microorganisms, or “microbiota”, inhabit the gut and affect its homeostasis, influenc... more Billions of microorganisms, or “microbiota”, inhabit the gut and affect its homeostasis, influencing, and sometimes causing if altered, a multitude of diseases. The genomes of the microbes that form the gut ecosystem should be summed to the human genome to form the hologenome due to their influence on human physiology; hence the term “microbiome” is commonly used to refer to the genetic make-up and gene–gene interactions of microbes. This review attempts to provide insight into this recently discovered vital organ of the human body, which has yet to be fully explored. We herein discuss the rhythm and shaping of the microbiome at birth and during the first years leading up to adolescence. Furthermore, important issues to consider for conducting a reliable microbiome study including study design, inclusion/exclusion criteria, sample collection, storage, and variability of different sampling methods as well as the basic terminology of molecular approaches, data analysis, and clinical i...
Studies on interleukin-8 receptor expression in ovine neutrophils
18th meeting of the …, 2000
... SFX Query. Items in AIR are protected by copyright, with all rights reserved, unless otherwis... more ... SFX Query. Items in AIR are protected by copyright, with all rights reserved, unless otherwise indicated. Share this record with your favourite social network: Del.icio.us, Citeulike, Connotea, Facebook, Stumble it! reddit, Browser ...
Isolation stress in sheep. Effects on neutrophilic gene expression of CD18-IL-8 and C5a receptors; Stress da isolamento nella pecora. Effetto sull'espressione genica …
Atti della Societa'Italiana …, 2001
... Original title, Stress da isolamento nella pecora. ... ANIMAL DOMESTIQUE, ANIMAL UTILE, BETAI... more ... Original title, Stress da isolamento nella pecora. ... ANIMAL DOMESTIQUE, ANIMAL UTILE, BETAIL, BIOLOGIE, BOVIDAE, CAPRINAE, CATECHOLAMINE, CELLULE, CELLULE SANGUINE, COMPOSE AMINE ... URL: http://www.ismea.it/flex/FixedPages/IT/RicercaStampa.php/L/IT. ...
Additional file 2 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing
Additional file 2: Table S2. Instruments information. For each instrument used in this work, the ... more Additional file 2: Table S2. Instruments information. For each instrument used in this work, the model, the short name (used in manuscript, tables and figure), the sensitivity and the location are reported.
Additional file 3 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing
Additional file 3: Table S3. Strains melting temperatures. The instrument used for the HRM analys... more Additional file 3: Table S3. Strains melting temperatures. The instrument used for the HRM analysis, the operator who performed the HRM analysis, the primer set used, the melting temperature replicates (T1, T2 and T3) and their average melting temperature (aTm) are reported for each strain.
Additional file 1 of MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data
Additional file 1: This file contains a detailed description of the clustering algorithm, of the ... more Additional file 1: This file contains a detailed description of the clustering algorithm, of the input file and of each output file created by the tool.
Cytoskeleton actin changes in IL-2 activated cells
European Journal of Histochemistry, 2009
In the present study we analysed the changes in cytoskeletal actin in lymphoid cells following IL... more In the present study we analysed the changes in cytoskeletal actin in lymphoid cells following IL-2 activation and during cell interactions by means of light and electron microscopy, immunofluorescence and molecular analysis. By morphological analysis we observed a higher fluorescence in the activated cells than in the quiescent ones with no modifications in the cytoskeleton pattern comparing activated to resting cells. The results of molecular analysis indicate that, after IL-2 activation, there is a reorganisation of the actin component of the cell cytoskeleton accompanied by the differential expression of the corresponding genes. A future study will be extended to the analysis of others components of the cytoskeleton network.
Bacterial populations inhabiting a variety of natural and human-associated niches have the abilit... more Bacterial populations inhabiting a variety of natural and human-associated niches have the ability to grow in the form of biofilms. A large part of pathological chronic conditions, and essentially all the bacterial infections associated with implanted medical devices or prosthetics, are caused by microorganisms embedded in a matrix made of polysaccharides, proteins, and nucleic acids. Biofilm infections are generally characterized by a slow onset, mild symptoms, tendency to chronicity, and refractory response to antibiotic therapy. Even though the molecular mechanisms responsible for resistance to antimicrobial agents and host defenses have been deeply clarified, effective means to fight biofilms are still required. Lactic acid bacteria (LAB), used as probiotics, are emerging as powerful weapons to prevent adhesion, biofilm formation, and control overgrowth of pathogens. Hence, using probiotics or their metabolites to quench and interrupt bacterial communication and aggregation, and...
The establishment of gut microbiota is reportedly aberrant in newborns admitted to neonatal inten... more The establishment of gut microbiota is reportedly aberrant in newborns admitted to neonatal intensive care units (NICUs), with detrimental long-term health impacts. Here, we vertically tracked the developing gut bacterial communities of newborns hosted in an NICU during an outbreak sustained by ESBL Klebsiella pneumoniae and compared colonized and noncolonized patients. Most communities were highly variable from one sampling point to the next, and dominated by few taxa, often Proteobacteria and Enterobacteriaceae, with marked interindividual variability. This picture was retrieved independently of colonization status or clinical covariates. Our data support the emerging idea of preterm infants as a population in which no defined microbial signatures are clearly associated to clinical status. Instead, the strong pressure of the nosocomial environment, antibiotics and, in this case, the ongoing outbreak, possibly drive the evolution of microbiota patterns according to individual condi...
Background The rapid identification of pathogen clones is pivotal for effective epidemiological c... more Background The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable for fast and inexpensive pathogen typing protocols. Unfortunately, the mathematical/informatics skills required to analyse HRM data for pathogen typing likely limit the application of this promising technique in hospital settings. Results MeltingPlot is the first tool specifically designed for epidemiological investigations using HRM data, easing the application of HRM typing to large real-time surveillance and rapid outbreak reconstructions. MeltingPlot implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. The tool also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological investigations and it runs in a few seconds even w...
ObjectivesSubspecies pathogen typing is a pivotal tool to detect the emergence of high-risk clone... more ObjectivesSubspecies pathogen typing is a pivotal tool to detect the emergence of high-risk clones in hospital settings and to limit their spreading among patients. Unfortunately, the most used subspecies typing methods (i.e. Pulsed-field Gel Electrophoresis - PFGE, Multi-Locus Sequence Typing - MLST and Whole Genome Sequencing - WGS) are too expensive and time consuming to be suitable for real-time surveillance. Here we present Hypervariable-Locus Melting Typing (HLMT), a novel subspecies typing approach based on High Resolution Melting (HRM) analysis, which allows pathogen typing in a few hours and with ∼5 euros per sample.MethodsHLMT types the strains by clustering them using melting temperatures (HLMT-clustering) and/or by assigning them to Melting Types (MTs) on the basis of a reference dataset (HLMT-assignment). We applied HLMT (clustering and typing) to 134 Klebsiella pneumoniae strains collected during outbreaks or surveillance programs in four hospitals. Then, we compared H...
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