1,720,961 research outputs found
Next Generation Sequencing-based detection and characterization of microbial pathogens causing invasive infections and outbreaks in ICU: towards improved management of the high-risk patient
No full textHealthcare-associated infections (HAIs), often exacerbated by resistance to last-resource antimicrobials (AMR), are a major global threat, as documented by the new European Recommendation on Combating AMR. Considering the state-of-art scientific innovations and common issues (time, cost) related current diagnostic, the goal of this project is to develop a molecular approach for the detection and characterization of microorganisms causing invasive infections and outbreaks in ICUs and surgery using WGS.
During the project, different microorganisms (bacteria and mycetes) were selected for WGS performed adopting two different approaches: i) long-read sequencing, using the Oxford Nanopore MinION (ONT, Oxford, UK) ii) short-read sequencing, using Illumina platforms in outsourcing. In this project, WGS, was applied in four key fields:
1. Novel strategies for pathogen identification: in two invasive infections mediated by Gordoniae terrae and Salmonella tiphy, not identifiable by standard methods, WGS enabled rapid pathogen identification, demonstrating how the introduction of this technology in the clinical microbiology laboratory can play an important role in supporting diagnosis and appropriate treatment, improving patients’ outcome.
2. Typing of microbial agents of Public Health concern: M. bovis Bacillus Calmette-Guérin (BCG) is a strain of mycobacterium closely related to M. tuberculosis, which can be administered intravesically for the treatment of transitional cell carcinoma of the urinary bladder. Nevertheless, BCG immunotherapy has been associated with some adverse reactions, that can be observed after months or years. Long-read sequencing of strain BCG-GE, isolated from a patient admitted to a tertiary-care hospital in Albenga (Savona, Italy), previously subjected to BCG instillation with the OncoTice strain (Merck, US), yielded a complete genome and allowed identified as M. tuberculosis var. bovis BCG and a global phylogenetic analysis including other BCG strains. Results showed that BCG-GE was highly related with the BCG Tice strain, commonly employed in immunotherapy practices, demonstrating that the vertebral osteomyelitis was most an adverse event following BCG instillation.
3. Tracking of nosocomial outbreaks and genomic surveillance: the WGS-based tracking of a difficult-to-control nosocomial outbreak of Candida auris in San Martino Hospital (HSM), where it first emerged in 2019, revealed that all cases belonged to the clade I (South Asian), and that some putative cases no longer occurred as part of a defined outbreak. Typing of antifungal resistance markers revealed that resistance to echinocandins likely emerged following selection of FKS1S639F and FKS1F635Y mutants upon prolonged exposure to caspofungin and/or anidulafungin.
4. Detection of novel antimicrobial resistance mechanisms: WGS-based typing of a Klebsiella pneumoniae strains (NE 368) of clinical origin, testing resistant to ceftazidime/avibactam, revealed the presence of a blaKPC gene encoding a novel 270-loop mutated variant of KPC-3 (KPC-109). Cloning experiments demonstrated that KPC-109 production mediated resistance/decreased susceptibility to avibactam-based combinations (with ceftazidime, cefepime, and aztreonam) and cefiderocol, with a trade-off on resistance to carbapenems. However, in the presence of porin alterations commonly found in high-risk clonal lineages of K. pneumoniae, KPC-109 was able to confer clinical-level resistance to carbapenems. These findings expanded the current knowledge of the diversity of emerging variants of the KPC enzyme with 270-loop alterations that can be found in the clinical setting.
In conclusion, WGS is a key tool in many areas of clinical microbiology, providing microbiologists and clinicians with rapid and valuable information not available by other commercial methods. To date, however, several limitations to the application of WGS in clinical microbiology persist, for which the near future envisions the integration of library preparation, sequencing, and data analysis into a single efficient workflow, allowing implementation in the laboratory routine
Antimicrobial Activity of Glycine Air Polishing: A Clinical Split- Mouth Study on Full-Arch Implant-Supported Rehabilitations
No full textPurpose: To investigate the possible antimicrobial activity of glycine air polishing by comparing peri-implant microbiota before and after treatment. Materials and methods: A total of 15 patients who received implant-supported full-arch fixed rehabilitations were included. After prosthesis removal (T0), Plaque Index (PI), probing depth (PD), and bleeding on probing (BOP) were recorded. In each hemiarch, the implant with the highest PD score was selected for microbiologic sample collection from the peri-implant sulcus (T0). All patients received two different hygienic protocols (randomly administered, one per each hemiarch): glycine air-polishing (G) and cleansing with cotton pellets soaked in saline (C). At 7 days (T1) and 3 months (T2) after the intervention, PI and BOP were recorded, and new microbiologic samples were taken. Traditional polymerase chain reaction (PCR) and quantitative PCR real-time were employed for microbiologic analysis to investigate how the presence of different bacterial species varied according to the hygienic treatment performed. Results: Treatment G provided a significantly higher PI score reduction around implants compared to treatment C (P = .015). No statistical difference was found in the microbial population around G and C implant sites, with Tannerella forsythia being the most commonly detected bacterial species in both G and C groups. No statistical differences were found between the antimicrobial activity of treatments C and G. Conclusions: Glycine powder air polishing is a valid method for professional hygienic care of implants and was more effective in PI reduction compared to the control treatment. However, its antimicrobial efficacy cannot be confirmed by the outcomes of the present study
Levels of beta-D-glucan in Candida auris supernatants, an in vitro and in vivo preliminary study
No full textSerum (1,3)-beta-d-glucan (BDG) assay is a non-culture-based test recommended for the diagnosis of invasive candidiasis owing to its faster results and higher sensitivity than blood cultures. Its performance might vary for different Candida species. The aim of this study was to determine in vitro levels of BDG in Candida auris culture supernatants and evaluate BDG levels in patients with C. auris candidemia sustained by these stains
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
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
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
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