1,721,107 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Living together in a world of extended-spectrum cephalosporin resistance: molecular snapshots of a complex epidemiology
No full textExtended-spectrum cephalosporinase (ESCase)-producing Enterobacteriaceae from human and animal origin have emerged worldwide during the last decades. Although studies documenting direct transmission between humans and animals are rare, the existence of shared reservoirs of extended-spectrum cephalosporinase genes, plasmids and/or STs suggests cross-transmissions and raises the concern of a possible zoonotic source of ESBL/AmpC-producers for humans. The aim of this thesis is to explore the molecular relatedness of extended-spectrum cephalosporin (ESC)-resistant Enterobacteriaceae of human and animal origin and assess their cross-transmission and epidemiology from a “One health” perspective. Chapter 1, as an introduction provides the necessary background information of the extended-spectrum cephalosporinase-producing Enterobacteriaceae and their complex epidemiology, to offer a better understanding of the studies presented in this thesis. Chapter 2 focuses on the emergence and the molecular characteristics of ESC-resistant Salmonella enterica serotype Heidelberg isolates in the Netherlands. Their recent emergence was attributed to food-producing animals and poultry products imported from Brazil, while no human infections linked to these contaminated animals and products have been yet documented in the Netherlands (Chapter 2a). In addition, the potential contribution of Kelp gulls of the southern hemisphere in the dissemination of ESC-resistant S. Heidelberg and other Enterobacteriaceae is presented (Chapter 2b). In Chapter 3, Enterobacteriaceae transmission among humans and between humans and animals is discussed. A cross-sectional study among Dutch preschool children and their parents is presented (Chapter 3a), describing the molecular characteristics of the recovered ESC-resistant Enterobacteriaceae and the frequency of intra-familial colonization with identical isolates. The longitudinal presence and molecular diversity of ESC-resistant E. coli from humans and pigs within the same pig farms are presented, confirming transmission events between farmers and their pigs (Chapter 3b). In Chapter 4, SHV extended-spectrum β-lactamases are discussed. The global epidemiology of Enterobacteriaceae encoding SHV ESCases is reviewed in Chapter 4a, highlighting the ubiquity of these extended-spectrum cephalosporinases. Finally, the recent association of blaSHV-12 with IncX3 plasmids among E. coli isolates in the Netherlands, as well as the genetic and functional characteristics of these plasmids contributing to blaSHV-12 emergence are reported (Chapter 4b). In the general discussion (Chapter 5), the results of the thesis are presented and discussed in relation to the epidemiology of ESC-resistant Enterobacteriaceae and the available international literature. Major outcomes of the studies presented in this thesis, using the available molecular microbiology techniques and the incorporation of human and animal components in a “One Health” approach, provide insights on emerging trends among ESC-resistant Enterobacteriaceae of human and animal origin, their cross-transmission within and between reservoirs, as well as the complexity of their “One Health” epidemiology in order to assess the role of animals as a relevant source of such resistant bacteria for humans
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Evolutionary Genetics of ESBL/pAmpC-producing Escherichia coli and Salmonella enterica from Poultry
No full textBackground: Third and fourth generation cephalosporins are listed by the World Health Organization as critically important antimicrobials, with the highest priority for human medicine. The main mechanism of resistance to third and fourth generation cephalosporins, also referred to as Extended Spectrum Cephalosporins (ESC), is degradation of the antimicrobial by enzymes. In species of Enterobacteriaceae, different families of Extended Spectrum Beta-Lactamases (ESBL) and plasmid-mediated AmpC beta-lactamases (pAmpC) are the most predominant enzymes. In poultry and poultry products, occurrence of ESBL/pAmpC in isolates of Escherichia coli and Salmonella enterica has been extensively described. Therefore, poultry has been suggested as a reservoir of ESBL/pAmpC-producing E. coli and Salmonella causing infections in humans. Data of ESBL/pAmpC-producing E. coli and Salmonella from poultry is scarce in Latin America. A research-driven initiative for integrated surveillance of Antimicrobial Resistance (AMR) was introduced in Colombian poultry production. Before this initiative, data on the status of AMR in agricultural settings was absent in the country. Aims of the research: The aims of the present thesis were i) to describe an initiative to develop an integrated program on AMR surveillance in Colombia; ii) to provide a highly-detailed characterization of ESBL/pAmpC genetic determinants in E. coli and S. enterica from poultry; iii) to reflect on the impact of poultry farming and commerce in the dissemination of ESBL/pAmpC. Results: The description of an initial consortium of stakeholders for the initiative of an integrated surveillance system in Colombia was provided (Chapter 2). From this initiative, baseline data of resistance to ESC was collected for Salmonella and E. coli. As a result, high level of similarity of ESBL/pAmpC genes and carrying plasmids was observed within E. coli (Chapter 3) and Salmonella (Chapter 4) in the country. Some gene-plasmid combinations were common between E. coli and Salmonella (e.g. blaCMY-2-IncI1 and blaSHV-12-IncI1) (Chapter 5). Overall, the combination of blaCMY-2 and IncI1/Sequence Type (ST) 12 plasmids was the most prevalent, and a high genomic relatedness was found among these plasmids within and between E. coli and Salmonella from Colombia and from other countries (Chapter 5). A marked geographical clustering within the most prevalent Salmonella serovar-STs in Colombia, S. Paratyphi B variant Java (here referred as S. Java) ST28 and S. Heidelberg ST15 was observed (Chapter 4). Subsequent analysis including S. Java ST28 genomes from other Latin American countries, showed high level of genomic relatedness across Latin American countries, indicating the circulation of a conserved clone of S. Java ST28 within the region (Chapter 6). Conclusions: In E. coli in poultry from Colombia and other countries, dissemination of ESBL/pAmpC is mainly mediated by transfer of genes and plasmids. In S. enterica from Colombia, dissemination is mainly mediated by clonal spread of genes, plasmids and strains combined. The dissemination within and between countries of poultry-associated ESBL/pAmpC can occur due to common practices of poultry farming and commerce. In order to measure the success of future interventions against AMR, it is necessary to implement integrated surveillance systems at national scale in Latin American countries
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Living together in a world of extended-spectrum cephalosporin resistance: molecular snapshots of a complex epidemiology
No full textExtended-spectrum cephalosporinase (ESCase)-producing Enterobacteriaceae from human and animal origin have emerged worldwide during the last decades. Although studies documenting direct transmission between humans and animals are rare, the existence of shared reservoirs of extended-spectrum cephalosporinase genes, plasmids and/or STs suggests cross-transmissions and raises the concern of a possible zoonotic source of ESBL/AmpC-producers for humans. The aim of this thesis is to explore the molecular relatedness of extended-spectrum cephalosporin (ESC)-resistant Enterobacteriaceae of human and animal origin and assess their cross-transmission and epidemiology from a “One health” perspective. Chapter 1, as an introduction provides the necessary background information of the extended-spectrum cephalosporinase-producing Enterobacteriaceae and their complex epidemiology, to offer a better understanding of the studies presented in this thesis. Chapter 2 focuses on the emergence and the molecular characteristics of ESC-resistant Salmonella enterica serotype Heidelberg isolates in the Netherlands. Their recent emergence was attributed to food-producing animals and poultry products imported from Brazil, while no human infections linked to these contaminated animals and products have been yet documented in the Netherlands (Chapter 2a). In addition, the potential contribution of Kelp gulls of the southern hemisphere in the dissemination of ESC-resistant S. Heidelberg and other Enterobacteriaceae is presented (Chapter 2b). In Chapter 3, Enterobacteriaceae transmission among humans and between humans and animals is discussed. A cross-sectional study among Dutch preschool children and their parents is presented (Chapter 3a), describing the molecular characteristics of the recovered ESC-resistant Enterobacteriaceae and the frequency of intra-familial colonization with identical isolates. The longitudinal presence and molecular diversity of ESC-resistant E. coli from humans and pigs within the same pig farms are presented, confirming transmission events between farmers and their pigs (Chapter 3b). In Chapter 4, SHV extended-spectrum β-lactamases are discussed. The global epidemiology of Enterobacteriaceae encoding SHV ESCases is reviewed in Chapter 4a, highlighting the ubiquity of these extended-spectrum cephalosporinases. Finally, the recent association of blaSHV-12 with IncX3 plasmids among E. coli isolates in the Netherlands, as well as the genetic and functional characteristics of these plasmids contributing to blaSHV-12 emergence are reported (Chapter 4b). In the general discussion (Chapter 5), the results of the thesis are presented and discussed in relation to the epidemiology of ESC-resistant Enterobacteriaceae and the available international literature. Major outcomes of the studies presented in this thesis, using the available molecular microbiology techniques and the incorporation of human and animal components in a “One Health” approach, provide insights on emerging trends among ESC-resistant Enterobacteriaceae of human and animal origin, their cross-transmission within and between reservoirs, as well as the complexity of their “One Health” epidemiology in order to assess the role of animals as a relevant source of such resistant bacteria for humans
I-complex plasmids – a story about incompatibility and host adaptation.
No full textAntimicrobial resistance (AMR) is a growing problem worldwide. This is mainly the result of the presence of resistance genes in bacteria. When these genes are located in small pieces of DNA, so called plasmids, they can easily spread between bacteria. This thesis gives an overview the different types of plasmids, all with their different resistance genes, and their presence around the globe. Bacteria may contain a number of different plasmids in a single cell. whether any of these plasmids can be stably maintained depends on several factors. One of these factors is called incompatibility, which is the inability of plasmids to be maintained in one cell. Based on this incompatibility plasmids can be categorized in 40 different “Inc” groups, a biological phenomenon that was long used as a typing system to study epidemiology. This thesis focusses on the members of the “I-complex” incompatibility group, found in Enterobacteriaceae and frequently associated with important resistance gene classes such as the so-called Extended Spectrum Beta-lactamases (ESBLs). The I-complex includes IncI1α, IncI1γ, IncI2, IncK, IncB/O and IncZ plasmids. In this thesis the basis of their incompatibility is analysed and the results show that a single mutation (change in DNA) can determine if two plasmids are compatible or not. It concludes that IncB/O and IncZ plasmids, which were previously considered compatible and thus different plasmids, were actually incompatible and should be considered as highly similar. It also shows that the IncK plasmid group, which is an important carrier of resistance genes in human and poultry bacteria, consists of two compatible plasmid lineages, designated IncK1 and IncK2. Studies into the molecular effects of these plasmid types on the physiology of their host cell showed that IncK2 plasmids provide a fitness advantage at a higher environmental temperature which may have resulted in their predominance in poultry over IncK1, which is mostly found in mammals. Overall, the results presented in this thesis highlight the importance of plasmids in the spread of AMR, and it underlines the importance of understanding the plasmid compatibility and its adaptation to the bacterial or animal host
Plasmid mediated quinolone resistance in Enterobacteriaceae
No full textThis thesis describes the occurrence of Plasmid Mediated Quinolone Resistance (PMQR) in Salmonella and E. coli from The Netherlands and other European countries. Furthermore, the genetic background of these genes was characterized. Fluoroquinolones are widely used antibiotics in both human and veterinary medicine. Resistance to fluoroquinolones is considered to be a risk for human health and is mainly caused by chromosomal mutations in topoisomerase genes. Since 1998, different types of PMQR emerged encoded by different resistant genes: qnrA, qnrS, qnrB, qnrC, qnrD, aac(6’)-1b-cr, oqxAB and qepA. PMQR in Enterobacteriaceae results in reduced susceptibility to (fluoro)quinolones to levels below clinical breakpoints. However, PMQR is considered clinically relevant because it facilitates the acquisition of full quinolone resistance. In a national study, the earliest identified PMQR-positive Salmonella isolate in The Netherlands was a human qnrS1-positive S. Corvallis isolate obtained in 2003. Furthermore, eight different Salmonella serovars were found harbouring different PMQR genes (qnrS1, qnrB2 and qnrB19). Almost all isolates were of human origin. Further study revealed the presence of PMQR genes on different plasmid families, including IncN plasmids carrying qnrS1, qnrB2 or qnrB19. But also qnrS1 on ColE, IncR or incHI2 plasmids. The majority of these plasmids were self-transferable by conjugation. However, PMQR-genes were also present on smaller non-conjugative plasmids.More recently, a continuous low prevalence of PMQR-suspected Salmonella isolates was observed in The Netherlands with a slight tendency to increase. The earliest identified PMQR-positive E. coli in animals from The Netherlands was a qnrS1-carrying E. coli obtained from a broiler obtained in 2009. To date, the prevalence of PMQR-suspected E. coli in food-producing animals in The Netherlands is low and only observed in broilers and veal calves. A European study demonstrated a low prevalence of PMQR-positive Salmonella isolates, with qnrS1, qnrB19 and qnrB2 as the predominant PMQR-determinants identified. The rare qnrD1 was identified in eight different serovars from three different countries. This study demonstrated a wide spread of PMQR genes in Europe among Salmonella from different sources despite the low prevalence and it suggest poultry to be the main source for PMQR-determinants in Salmonella. Similar to Salmonella, the prevalence of PMQR was low in E. coli with predominant variant qnrS1 in isolates from poultry (Gallus gallus and turkeys). Antibiotic resistant bacteria can spread over great distances via travel of people or transport of animals, but also by the worldwide trade in food and feed. In this thesis two examples of import of multidrug resistant Enterobacteriaceae are discussed: PMQR-positive, multidrug resistant Salmonella obtained in humans originated from or had a travel history to the African continent and PMQR-positive, multidrug resistant Enterobacteriaceae identified on culinary herbs from Southeast Asia. Despite the strong reduction of fluoroquinolone usage in animals in The Netherlands, resistance is still high in commensal E. coli and Campylobacter spp. in some food-producing animal species. Although fluoroquinolone resistance is mainly caused by chromosomal mutations, PMQR complicates the development and spread of fluoroquinolone resistance which makes it important to include this in the surveillance
I-complex plasmids – a story about incompatibility and host adaptation.
No full textAntimicrobial resistance (AMR) is a growing problem worldwide. This is mainly the result of the presence of resistance genes in bacteria. When these genes are located in small pieces of DNA, so called plasmids, they can easily spread between bacteria. This thesis gives an overview the different types of plasmids, all with their different resistance genes, and their presence around the globe. Bacteria may contain a number of different plasmids in a single cell. whether any of these plasmids can be stably maintained depends on several factors. One of these factors is called incompatibility, which is the inability of plasmids to be maintained in one cell. Based on this incompatibility plasmids can be categorized in 40 different “Inc” groups, a biological phenomenon that was long used as a typing system to study epidemiology. This thesis focusses on the members of the “I-complex” incompatibility group, found in Enterobacteriaceae and frequently associated with important resistance gene classes such as the so-called Extended Spectrum Beta-lactamases (ESBLs). The I-complex includes IncI1α, IncI1γ, IncI2, IncK, IncB/O and IncZ plasmids. In this thesis the basis of their incompatibility is analysed and the results show that a single mutation (change in DNA) can determine if two plasmids are compatible or not. It concludes that IncB/O and IncZ plasmids, which were previously considered compatible and thus different plasmids, were actually incompatible and should be considered as highly similar. It also shows that the IncK plasmid group, which is an important carrier of resistance genes in human and poultry bacteria, consists of two compatible plasmid lineages, designated IncK1 and IncK2. Studies into the molecular effects of these plasmid types on the physiology of their host cell showed that IncK2 plasmids provide a fitness advantage at a higher environmental temperature which may have resulted in their predominance in poultry over IncK1, which is mostly found in mammals. Overall, the results presented in this thesis highlight the importance of plasmids in the spread of AMR, and it underlines the importance of understanding the plasmid compatibility and its adaptation to the bacterial or animal host
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