The evolution and propagation of antibiotic resistance by bacterial pathogens are significant threats to global public health. Contemporary DNA sequencing tools were applied here to gain insight into carriage of antibiotic resistance genes in Escherichia coli, a ubiquitous commensal bacterium in the gut microbiome in humans and many animals, and a common pathogen. Draft genome sequences generated for a collection of 101 E. coli strains isolated from healthy undergraduate students showed that horizontally acquired antibiotic resistance genes accounted for most resistance phenotypes, the primary exception being resistance to quinolones due to chromosomal mutations. A subset of 29 diverse isolates carrying acquired resistance genes and 21 control isolates lacking such genes were further subjected to long-read DNA sequencing to enable complete or nearly complete genome assembly. Acquired resistance genes primarily resided on F plasmids (101/153 [67%]), with smaller numbers on chromosomes (30/153 [20%]), IncI complex plasmids (15/153 [10%]), and small mobilizable plasmids (5/153 [3%]). Nearly all resistance genes were found in the context of known transposable elements. Very few structurally conserved plasmids with antibiotic resistance genes were identified, with the exception of an ∼90-kb F plasmid in sequence type 1193 (ST1193) isolates that appears to serve as a platform for resistance genes and may have virulence-related functions as well. Carriage of antibiotic resistance genes on transposable elements and mobile plasmids in commensal E. coli renders the resistome highly dynamic. IMPORTANCE Rising antibiotic resistance in human-associated bacterial pathogens is a serious threat to our ability to treat many infectious diseases. It is critical to understand how acquired resistance genes move in and through bacteria associated with humans, particularly for species such as Escherichia coli that are very common in the human gut but can also be dangerous pathogens. This work combined two distinct DNA sequencing approaches to allow us to explore the genomes of E. coli from college students to show that the antibiotic resistance genes these bacteria have acquired are usually carried on a specific type of plasmid that is naturally transferrable to other E. coli, and likely to other related bacteria.
To date, sustainable development has been the most important discourse informing planning, a powerful rhetoric for solving environmental problems that shows confidence in human ingenuity and technological advancements. However, recent advances in information and communication technologies, are prompting the development of smart(er) approaches to (sustainable) development, which might be signifying a departure from the more traditional, or perhaps earlier, greener narratives underpinning sustainable development. Within this context and informed by analysis of the literature, this paper aims to reflect on the extent to which ideas of going green and going smart are converging or diverging from the path towards sustainable development. This is done using convergence theory and Bennet's typology (1991) of similarities as an analytical framework. The findings suggest that the convergence of greening and smart ideas for sustainable development might be better achieved if smart-centric approaches to policy-and planning are subsumed in the overarching vision of environmental quality and resilience, with green approaches to urban development setting the path and driving decisions towards a sustainable future.
a b s t r a c t a r t i c l e i n f oThe strengthening of spatial database infrastructures, further promoted by the INSPIRE Directive adopted in 2007, has led to an increased use of spatial data in planning and decision-making. Given that land-use plans are intrinsically spatial, such evidence and approaches can significantly benefit plan-making. A spatial framework could especially support the specific Strategic Environmental Assessment (SEA) aspects of the plan-making process. Spatial tools such as Geographic Information Systems (GIS) are particularly well-placed to support the environmental integration sought in SEA by providing evidence through the spatial assessment of multiple environmental datasets. Moreover, GIS bring the opportunity to augment conventional assessment techniques (e.g. matrix-based assessments) by acting as visual mediators of spatial knowledge and by providing an effective tool for the spatial and temporal analysis of environmental impacts. This paper presents a GIS-based approach to SEA (GISEA), and analyses the above premise by evaluating the barriers, limitations, opportunities and benefits of its implementation. The GISEA approach has been applied to seven development plans of differing scales in the Republic of Ireland. The results of the case studies revealed that current issues in SEA (e.g. restricted time-frames and institutional arrangements) condition the implementation of a GIS-based approach. Moreover, GIS expertise, data accessibility and quality remain limiting factors to an effective GIS application in SEA. However, the results also confirmed that GIS have the potential to increase the objectivity and accuracy of the assessment, enhance both the understanding of environmental and planning considerations and the delivery of information, and, therefore, help to improve the effectiveness of SEA practice.
Malassezia pachydermatis is a basidiomycetous yeast that causes infections in humans and animals. Here, we report the genome sequence of Malassezia pachydermatis strain CBS 1879, which will facilitate the study of mechanisms underlying pathogenicity of the only non-lipid-dependent Malasezzia species.
The species constituting the genus Malassezia are considered to be emergent opportunistic yeasts of great importance. Characterized as lipophilic yeasts, they are found in normal human skin flora and sometimes are associated with different dermatological pathologies. We have isolated seven Malassezia species strains that have a different Tween assimilation pattern from the one typically used to differentiate M. furfur, M. sympodialis, and M. slooffiae from other Malassezia species. In order to characterize these isolates of Malassezia spp., we studied their physiological features and conducted morphological and molecular characterization by PCR-restriction fragment length polymorphism and sequencing of the 26S and 5.8S ribosomal DNA-internal transcribed spacer 2 regions in three strains from healthy individuals, four clinical strains, and eight reference strains. The sequence analysis of the ribosomal region was based on the Blastn algorithm and revealed that the sequences of our isolates were homologous to M. furfur sequences. To support these findings, we carried out phylogenetic analyses to establish the relationship of the isolates to M. furfur and other reported species. All of our results confirm that all seven strains are M. furfur; the atypical assimilation of Tween 80 was found to be a new physiological pattern characteristic of some strains isolated in Colombia.The genus Malassezia comprises lipophilic yeasts found in the normal flora of human skin and other mammals. These yeasts were described by Eichstedt in 1848 as being associated with pityriasis versicolor (PV) lesions (13). The taxonomy and nomenclature of the genus Malassezia was controversial for many decades. Indeed, until 1990 only three species were recognized: M. furfur, M. sympodialis, and M. pachydermatis, a non-lipid-dependent species (17,21,38 (4,6,11,17,18,20,21,26,34,38,(40)(41)(42).Malassezia species have been associated with diverse dermatological pathologies, including PV, seborrheic dermatitis dandruff, atopic dermatitis, folliculitis, psoriasis, onicomycosis, and blepharitis. M. furfur and M. pachydermatis have been associated with systemic infections in patients with underlying diseases and those receiving intravenous lipid emulsions (6, 7, 9-11, 16, 29, 33, 34).Although the role of Malassezia species in the development of these diseases is not clear, some authors suggest that M. globosa is the causal agent of PV, while others have found a greater percentage of isolates of M. sympodialis associated with the disease. Differences in diagnosis might be due to sampling methods and differences between the culture media used, leading to controversies in clinical studies of these dermatological pathologies (1, 7, 9, 10). New physiological patterns for identification have been described, and recently the availability of molecular biology and sequencing techniques has allowed the species to be distinguished more clearly (17-21). Despite the difficulty in isolating, maintaining, and identifying these yeasts, different characteristics of ...
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