1,721,394 research outputs found
Pan-genomic analysis of clonal bacterial samples using nanopore reads and genome graphs
Full text linkBacterial genetic variation originates through multiple mechanisms, including mutations during replication, movement of mobile elements, and various forms of recombination. As a result, genomes can be highly divergent with only a small fraction of genes core to all and a large pangenome of genes which have been identified in one or more sequenced samples.
In this context, the ability to accurately detect genetic variation throughout the pangenome and compare many genomes remains a difficult problem. Here we present a novel pangenome reference graph structure, which represents the known genetic variation within a species as a collection of `floating' graphs. Each of these represents some homologous region such as a cluster of genes. By approximating a sequenced genome as a mosaic of genomes from the reference panel, this design forms the basis for a systematic framework in which to analyse diverse sets of samples where a single reference would be inappropriate.
Applying this method to E. coli, we demonstrate how it enables us to describe genetic variation at both a coarse (gene presence) and a fine (SNP/indel) level. We demonstrate how this enables us to successfully compare divergent genomes within a species, gaining dramatically higher sensitivity to SNP variation than single reference-genome approaches. We go on to demonstrate how this method enables us to investigate global genetic variation in K. pneumoniae, and to describe the spectrum of allele frequencies in accessory genes.
The method works for either long Nanopore or short Illumina reads, and we hope will provide the basis for addressing many questions in diverse datasets.</p
Investigating the variability of virulence in natural populations of Staphylococcus aureus using whole genome sequencing
Full text linkInvasive Staphylococcus aureus disease is an important cause of morbidity and mortality, but is much rarer than asymptomatic carriage. The contribution of the bacterial genome to S. aureus infection is incompletely understood, and molecular epidemiology provides conflicting evidence. This thesis aims to improve our understanding of this contribution using the resolution afforded by whole-genome sequencing.
In a systematic study of S. aureus evolution in 105 hosts during invasive S. aureus disease, I demonstrate extensive within-host diversity, with evidence for varying selective pressures and within-host adaptation. Evidence for adaptation is strongest in genes under control of transcriptional regulatory systems, including Repressor of surface proteins (Rsp) (p=10â6.4) â a recently discovered global virulence regulator â and the Accessory gene regulator (Agr) (p=10â5.6), which are enriched for protein-altering variants 3.6- and 2.9-fold respectively. The development of invasive disease is associated with subtle changes in the transcriptional regulation of Staphylococcus aureus arising within hosts.
Applying recently developed tools for bacterial genome-wide association studies (GWAS), I present GWAS investigating for S. aureus genomic associations with two disease phenotypes: bacteraemia and pyomyositis. A study of S. aureus bacteraemia and carriage in 2001 isolates from the United Kingdom shows bacteraemia is not strongly bacterially determined: no lineages, genes or variants were significantly associated with bacteraemia.
In a study of 518 isolates from pyomyositis and carriage in Cambodian children, the presence of Panton-Valentine leukocidin (PVL) genes increases the odds of pyomyositis 130-fold (p=10â18), and variation in these genes and an adjacent promoter region are sufficient to explain over 99.9% of the heritability of pyomyositis. These results establish staphylococcal pyomyositis, like tetanus and diphtheria, as a disease depending critically on expression of a toxin.
Microbial genomics offers unparalleled opportunities to understand infections, and here I demonstrate insights generated through pathogen evolution within hosts and bacterial GWAS.</p
Staphylococcus aureus: the host-organism relationship
Full text linkStaphylococcus aureus is a worldwide leading cause of skin and soft tissue, bone and joint, and bloodstream infection. Despite this, S. aureus is also a harmless commensal in about one third of the population, although carriage is a risk factor for subsequent disease. S. aureus has evolved resistance to several antibiotics, including meticillin, resulting in meticillin-resistant S. aureus (MRSA), which in the UK largely consists of two epidemic lineages. In spite of much research, substantial aspects of the epidemiology and biology of S. aureus are still poorly understood.In investigating the S. aureus host-organism relationship, this thesis has three aims. To explore the interface between community and hospital-acquired S. aureus; to investigate the carriage dynamics of S. aureus in the community; and to use population genetic methods to study epidemic hospital associated S. aureus lineages.Case-control studies comparing hospital and community-acquired MRSA revealed that the majority of UK MRSA remains healthcare associated, with community-acquired MRSA reliably identified in only 0.2% of individuals. However, an additional 0.2% of individuals also carried "feral" MRSA with molecular characteristics identical to hospital-associated strains, but in hosts with no healthcare risk factors. To further investigate S. aureus carriage dynamics in the community, a carriage study was designed to collect detailed host factor information and correlate this with S. aureus carriage over time. In the study 32% of participants carried S. aureus of which the majority carried for over one year. Younger age was associated with transient carriage, including S. aureus acquisition in individuals who were initially negative. Finally, whole-genome sequencing of two epidemic S. aureus lineages indicated rapid clonal expansion of MRSA and clear geographic and temporal genetic structure. One particularly closely related cluster of strains may provide a genetic explanation for an MRSA outbreak in Brighton
Using genomic epidemiology to improve molecular diagnostics for Streptococcus pneumoniae and to study streptococcal population structure
No full textVarious Streptococcus species, including Streptococcus pneumoniae (pneumococcus), can asymptomatically colonise the human upper respiratory tract. Pneumococci can also cause life-threatening infections such as meningitis and pneumonia, constituting a large burden on global health. Using large bacterial genome datasets, this thesis aimed to improve nucleic acid amplification tests used to identify pneumococci and to enhance our understanding of the streptococcal population structure. First, I assessed the in silico performance of existing PCR-based diagnostics in 7,547 pneumococcal genomes and 1,825 genomes of 55 non-pneumococcal Streptococcus (NPS) species. I designed a new multiplex quantitative PCR (qPCR) assay targeting Xisco and SP2020 and validated this assay in vitro, finding high specificity, sensitivity, and accurate performance across a range of pneumococcal amplicons. Building on these results, I assessed the in silico performance of existing pneumococcal loop-mediated isothermal amplification (LAMP) assays, revealing cross-reactivity with up to ten NPS species. I designed and validated in vitro a highly sensitive, specific and fast new real-time LAMP assay targeting SP2020, which could be particularly useful in low-resource settings. Finally, I compiled a diverse Streptococcus genome dataset to investigate in silico differences across 105 species, including guanine-cytosine content and total assembly length. Using two different methods, I studied the size and function of the streptococcal core genome. Whilst seven single locus typing targets were unable to accurately stratify S. pneumoniae from closely related viridans streptococci, the phylogeny based on 412 streptococcal core genes provided a robust framework for mapping the in silico presence of antimicrobial resistance genes and virulence factors across the genus. This thesis harnessed the power of genomic data to improve pneumococcal diagnostic assays and to study differences between streptococcal species. The new multiplex qPCR and real-time LAMP assays can facilitate improved pneumococcal identification in clinical and research microbiology laboratories and the in silico plus in vitro methodology can be applied to improve diagnostics for other pathogens. The insights gained into streptococcal population structure contribute to an enhanced understanding of streptococcal evolution, epidemiology and virulence factor distribution
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Variations on the Author
Full text link“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
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe 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
Evaluating effects of antibiotic treatment on resistance and patient outcomes using linked microbiology and patient electronic health record data
Full text linkThere is substantial pressure on medical services to reduce antibiotic prescribing, aimed at reducing the spread of antimicrobial resistance. Reducing prescribing in the acute hospital setting provides unique challenges, with antibiotic decisions made in the first few hours of admission with uncertainty over both diagnosis and severity of illness. The potential benefit to the patient must be balanced with the risks of side-effects and of future resistant infections to both the patient and the population as a whole.
I first review the evidence currently available to the acute clinician to assist in this decision. I then conduct a small study of antibiotic use in the acute medical setting, demonstrating that whilst substantially reducing antibiotic initiation and prescribing is possible, this is at the cost of more admissions and longer length-of-stay. I highlight the need for larger studies to meaningfully assess clinical outcomes, including resistant infections.
I then perform two studies investigating the accuracy of electronic health record data. The first assesses to what degree diagnostic codes can be used to estimate Charlson comorbidities to enable risk-adjusted studies of clinical outcome, concluding that diagnostic coding is relatively robust. The second assesses the degree to which diagnostic codes can be used to identify infections and their bacterial cause, finding that careful data curation is required, and significant limitations exist in using coded data to study causative organisms.
I use results from these studies to inform the subsequent design of a study of patients with Escherichia coli and Klebsiella pneumoniae bloodstream infections using linked electronic health record data and laboratory microbiology results. I find that previous broad-spectrum beta-lactams and trimethoprim exposure are associated with beta-lactam resistance in these infections at the level of an individual patient, but no evidence of association between duration of antibiotic exposure and development of resistance.
This work supports current efforts to limit use of broad-spectrum antibiotics, particularly beta-lactams, and to encourage the clinician, if an antibiotic is required, to try and use narrow spectrum antibiotics. It also showcases the power of electronic health record data, if used carefully, to progress the current knowledge in identifying rational prescribing strategies to reduce development of antimicrobial resistance
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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