1,721,021 research outputs found
Phenotypic and genotypic characterisation of invasive Streptococcus pneumoniae expressing atypical capsular types
Get PDFAbstract Background: Streptococcus pneumoniae (pneumococcus) is one of the leading causes of morbidity and mortality. It accounts for over 500 000 case fatalities in children annually. Its invasive nature is not well understood; however, progress has been made with the discovery of the major virulence factor: the polysaccharide capsule. The biochemical properties of the capsule have allowed for the identification of more than 100 serotypes, resulting in the development of new, effective vaccines. However, in recent years, it has become challenging to identify serotypes, due to mutations in the capsular gene cluster of atypical isolates. The encoded capsules have been shown to cross react with anti-sera from other pneumococcal serogroups. We, therefore, aimed to phenotypically and genotypically characterise a subset of isolates collected from a nationwide surveillance program, exhibiting atypical serotyping results. Methods: A convenient sample of 68 atypical isolates were selected for the purpose of this study. Pneumococci were isolated and characterized using conventional microbiological laboratory techniques. Confirmed pneumococci were then subjected to antimicrobial susceptibility testing using the Kirby Bauer disk diffusion method and serotyped using the Quellung method. Genotypic characterization was conducted by analysing whole-genome sequencing data to reveal the in-silico serotype, multi-locus sequence type profiles, virulence factors, and antibiotic-resistance genes present, including whole genome sequencing-inferred minimum inhibitory concentration where applicable. Analysis of the capsular loci for single nucleotide polymorphism mutations were also conducted. Nuclear magnetic resonance was used to characterise the pneumococcal polysaccharide capsule. Results: Of all the pneumococci included in this study, 21% (14/68), 7% (5/68), 6% (4/68), 1% (1/68) of the isolates were resistant to tetracycline, chloramphenicol, azithromycin, and cefuroxime, respectively. Only 11% of the isolates were resistant to more than one drug. A total of 24 Sequence types (ST) were identified amongst the isolates. Ten of the isolates were identified as novel STs, and were thus assigned a unique ST. Among the 14 known STs, 12 have been known to be associated with invasive encapsulated pneumococci. ST9813 was the most prevalent ST. All isolates belonged to serogroup 35 (35A, 35B, 35C and 35F). The majority of isolates were primarily identified as serotype 35B, 72% (49/68) vs 59% (40/68) for the Quellung reaction and whole genome sequencing, respectively. Analysis of the capsular loci revealed the presence of 146 non-synonymous mutations in the capsule encoding biosynthetic genes. Nuclear magnetic resonance data was inconclusive, although electron microscopy revealed the presence of the polysaccharide capsule. Conclusions: Comparative genomics analysis revealed single nucleotide polymorphism mutations in the capsular biosynthetic genes, that may alter the production of the polysaccharide capsule; resulting in atypical behaviour observed within these strains. A high concordance rate between phenotypic and molecular tests was observed, and the utilization of both methods allowed for a detailed investigation of atypical pneumococcal isolates. There is a need for continued surveillance of atypical strains and optimisation of pneumococcal capsular extraction protocols, to further elucidate the chemical structure of these novel atypical strains of pneumococci
Prevalence and Molecular Epidemiology of Bordetella pertussis Infection in South Africa
No full textA research report submitted in fulfillment of the requirements for the Doctor of Philosophy, in the Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, 2024Pertussis remains a public health concern in South Africa, with increases in cases and outbreaks in recent years. We determined the incidence, transmission dynamics, serological attack rates and molecular epidemiology of B. pertussis in South Africa. Data from a longitudinal study enrolling individuals each year in 2016–2018 from two communities were used. Nasopharyngeal swabs were collected from participants twice-weekly and tested by real-time PCR. Serum was collected at 8 time points and tested using the anti-pertussis toxin IgG ELISA kit. Whole genome sequencing was performed on all available cultures (n=32) sourced from three additional surveillance programs between 2015–2019. Data were described and analyzed using univariate and multivariable regression models. Among 1684 participants, the incidence of B. pertussis was 0.21 (95% confidence interval 0.17–0.25) per 100 person-weeks. The mean duration of infection was 12 days (±standard deviation 19.1). Transmission of infection was more likely to occur from male index cases [adjusted odd ratio 12.20 (95%CI 1.57–94.96)], and individuals with ≥7 day’s infection duration [aOR 24.80 (95%CI 2.74–224.30)]. B. pertussis seroprevalence ranged from 1.8% to 5.2% across eight blood draws. The serological attack rate was 5.8% (87/1509), which was similar to the PCR attack rate (6.2%, 94/1509) (p=0.64). PCR-positive individuals aged 5–18 years (vs 19-44, aOR 6.8, 95% CI 1.3-35.1) and with episode duration of ≥7 days (vs <7 days, aOR 13.3, 95% vi CI 3.4-51.1) were more likely to seroconvert. For all individuals that seroconverted, the ≥4-fold rise in anti-PT IgG titer was detected by the next blood draw (mean: 2.9 months (range 3 weeks – 5.9 months). Using genome data, all isolates were identified as the globally-disseminated sequence type 2 and harbored the pertussis toxin promoter ptxP3. The dominant genotype was ptxP3-ptxA1-ptxB2-prn2-fimH2 (31/32, 96.9%), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Within the community, despite a high incidence of B. pertussis, there was an overall low seroprevalence. Our data highlighted that increases in cases in South Africa are not likely due to evolutionary changes in the genome but potentially waning immunity due to the use of acellular vaccines and/or population immunity gaps.MM202
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
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
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
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe 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
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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