scholarly journals A data compendium of Mycobacterium tuberculosis antibiotic resistance

2021 ◽  
Author(s):  
Alice Brankin ◽  
Kerri M Malone ◽  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genetic Mutation ◽  
Molecular Diagnostic ◽  
Whole Genome ◽  
Research Projects ◽  
Antitubercular Drugs ◽  
Resistance Prediction ◽  
To Come ◽  
New Research

The Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) presents here a global collection of 15,211 Mycobacterium tuberculosis clinical isolates, all of which have undergone whole genome sequencing and have had their minimum inhibitory concentrations to 13 antitubercular drugs measured. The isolates represent five major M. tuberculosis lineages originating from 23 countries across four continents. 6,814 isolates were found resistant to at least one drug, including 2,129 samples fully satisfy the clinical definitions of RR/MDR, pre-XDR or XDR. Resistance status to eight antitubercular drugs can be accurately predicted using a genetic mutation catalogue for over 90% of the isolates. Furthermore, we show the presence of suspected resistance conferring mutations for isolates resistant to the newly introduced drugs bedaquiline, clofazimine, delamanid and linezolid. Finally, a case study of rifampicin mono-resistance is presented to showcase how this compendium could be used to advance our genetic understanding of rare resistance phenotypes and evaluate the likely performance of a widely used molecular diagnostic tool. It is hoped that this compendium, the largest M. tuberculosis matched phenotypic and genotypic dataset to date, will facilitate and inspire new research projects for years to come.

scholarly journals Designing Collaborative Research: The Exploration of Common Purposes to Foster the Generation of Cross-Disciplinary Projects

2019 ◽  
Vol 1 (1) ◽  
pp. 2219-2228
Author(s):  
Juliette Brun ◽  
Chloé Salembier ◽  
Benjamin Loubet ◽  
Alexandra Jullien
Keyword(s):  
Design Process ◽  
Collaborative Research ◽  
Research Projects ◽  
Innovative Design ◽  
Organizational Issues ◽  
New Knowledge ◽  
Increasing Demand ◽  
New Research ◽  
Innovation Processes

AbstractDespite the increasing demand to develop cross-disciplinary research projects, designing collaborative research still prove to be difficult due to both scientific specialization and organizational issues. In this paper, we explore how innovative design dynamics can be developed between researchers to collectively build research projects that could become common purposes for collaboration. This work relies on a case study led with the newly formed Eco&Phy research team, who applied an innovative design process to initiate collaboration and design its scientific agenda for the next 5 years. This process was built based on both KCP and matching-building methodologies: it included an initialization phase, during which the team strategically chose topics to be explored, and exploration phases, during which researchers collectively developed new knowledge and concepts to build cross-disciplinary projects. At the end of the design process, the team had developed two new research lines that were integrated in its official agenda. In conclusion, the article discusses the relevance of design approaches to develop original collaborative research through dedicated innovation processes.

Report of The Delegates To The American Council of Learned Societies

PMLA ◽  
1935 ◽  
Vol 50 (4) ◽  
pp. 1342-1342
Author(s):  
Professor William A. Nitze
Keyword(s):  
International Research ◽  
Modern Language Association ◽  
Research Projects ◽  
Modern Language ◽  
American Council ◽  
Learned Societies ◽  
To Come ◽  
Recent Action ◽  
New Research

In the absence of the senior delegate, Professor Karl Young (Yale), Professor William A. Nitze (Chicago) reported on the American Council of Learned Societies. He dwelt on two aspects of the Council; one of which is the fact that, owing to the recent action of the Rockefeller Board, the Council can no longer look forward to active support from that quarter for encouragement in research. To be sure, the Board is financing the continuance of the offices of the Council during a period of three years. But the money for new research projects will presumably have to come from other sources—a circumstance that places an added responsibility of providing such funds on organizations like the Modern Language Association. Professor Nitze then gave an account of the 1935 meeting at Copenhagen of the Union académique internationale, which he attended (together with Mr. Leland) as a delegate of the A.C.L.S. He described the type of international research that the Union is now engaged in, and also reported the gratifying fact that the German and Austrian academies have been admitted to the Union by a formal vote.

scholarly journals Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Nilay Peker ◽  
Leonard Schuele ◽  
Nienke Kok ◽  
Miguel Terrazos ◽  
Stefan M. Neuenschwander ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Core Genome ◽  
Sequence Data ◽  
Complete Agreement ◽  
Whole Genome ◽  
First Line ◽  
Long Read ◽  
Drug Resistance Prediction ◽  
Resistance Prediction

Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) isolates can be used to get an accurate diagnosis, to guide clinical decision making, to control tuberculosis (TB) and for outbreak investigations. We evaluated the performance of long-read (LR) and/or short-read (SR) sequencing for anti-TB drug-resistance prediction using the TBProfiler and Mykrobe tools, the fraction of genome recovery, assembly accuracies and the robustness of two typing approaches based on core-genome SNP (cgSNP) typing and core-genome multi-locus sequence typing (cgMLST). Most of the discrepancies between phenotypic drug-susceptibility testing (DST) and drug-resistance prediction were observed for the first-line drugs rifampicin, isoniazid, pyrazinamide and ethambutol, mainly with LR sequence data. Resistance prediction to second-line drugs made by both TBProfiler and Mykrobe tools with SR- and LR-sequence data were in complete agreement with phenotypic DST except for one isolate. The SR assemblies were more accurate than the LR assemblies, having significantly (P<0.05) fewer indels and mismatches per 100 kbp. However, the hybrid and LR assemblies had slightly higher genome fractions. For LR assemblies, Canu followed by Racon, and Medaka polishing was the most accurate approach. The cgSNP approach, based on either reads or assemblies, was more robust than the cgMLST approach, especially for LR sequence data. In conclusion, anti-TB drug-resistance prediction, particularly with only LR sequence data, remains challenging, especially for first-line drugs. In addition, SR assemblies appear more accurate than LR ones, and reproducible phylogeny can be achieved using cgSNP approaches.

Transitioning Business for a Circular Economy

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Susan EVANS
Keyword(s):  
Professional Practice ◽  
Circular Economy ◽  
Radical Change ◽  
Virtual Space ◽  
Professional Experience ◽  
Operational Model ◽  
New Vision ◽  
To Come ◽  
Space Requirements

This case study explores the strategic business opportunities, for Lane Crawford, an iconic luxury department store, to transition in a circular economy towards sustainability. A new experimentation framework was developed and conducted among cross departmental employees, during a Design Lab, with intention to co-create novel Circular Economy business concepts towards a new vision: the later was a reframe of the old system based on the principles of sustainability; to move beyond a linear operational model towards a circular economy that can contribute to a regenerative society. This work draws on both academic and professional experience and was conducted through professional practice. It was found that innovative co-created concepts, output from the Design Lab, can create radical change in a circular economy that is holistically beneficial and financially viable; looking forward to extract greater value a)Internal organization requires remodeling to transform towards a circular economy; b)Requirement for more horizonal teams across departments vs solely vertical; c)New language and relationships are required to be able to transition towards a circular economy; d)Some form of physical and virtual space requirements, for cross-disciplinary teams to come together to co-create; e)Ability to iterate, learn and evolve requires agency across the business

Systemic Unsustainability as a Threat to Democracy

2020 ◽  
Author(s):  
Andrea Felicetti
Keyword(s):  
Research Agenda ◽  
Ecological Crisis ◽  
Illustrative Case ◽  
Sustainability Transition ◽  
Ways Of Thinking ◽  
Illustrative Case Study ◽  
New Research

Resilient socioeconomic unsustainability poses a threat to democracy whose importance has yet to be fully acknowledged. As the prospect of sustainability transition wanes, so does perceived legitimacy of institutions. This further limits representative institutions’ ability to take action, making democratic deepening all the more urgent. I investigate this argument through an illustrative case study, the 2017 People’s Climate March. In a context of resilient unsustainability, protesters have little expectation that institutions might address the ecological crisis and this view is likely to spread. New ways of thinking about this problem and a new research agenda are needed.

scholarly journals Molecular Detection of Mycobacterium tuberculosis in Oral Mucosa from Patients with Presumptive Tuberculosis

2020 ◽  
Vol 9 (12) ◽  
pp. 4124
Author(s):  
Barbara Molina-Moya ◽  
Nelly Ciobanu ◽  
Marta Hernandez ◽  
Cristina Prat-Aymerich ◽  
Valeriu Crudu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Oral Mucosa ◽  
The Elderly ◽  
Storage Conditions ◽  
Molecular Diagnostic ◽  
Smear Microscopy ◽  
X Rays ◽  
Rt Pcr ◽  
Tuberculosis Complex ◽  
Tb 34

Tuberculosis (TB) diagnosis is increasingly based on the detection of Mycobacterium tuberculosis complex (MTBC) DNA in sputum using molecular diagnostic tests as the first test for diagnosis. However, sputum can be difficult to obtain in children, patients without productive cough, and the elderly and approaches testing non-sputum samples are needed. We evaluated whether TB can be detected from the oral mucosa of patients with TB. Adults with presumptive TB were examined using culture, Xpert MTB/RIF, smear microscopy and X-Rays. Oral mucosa swabs collected on PrimeStore-MTM, stored at room temperature if tested within 30 days or at −20 °C if examined at a later time. RT-PCR was performed to detect M. tuberculosis DNA. Eighty patients had bacteriologically-confirmed TB, 34 had bacteriologically-negative TB (negative tests but abnormal X-rays) and 152 were considered not to have TB (not TB). Oral swabs RT-PCR were positive in 29/80 (36.3%) bacteriologically-confirmed, 9/34 (26.5%) bacteriologically-negative and 29/152 (19.1%) not TB. The yield varied among samples stored for less and more than 30 days (p = 0.013) from 61% (11/18) and 29% (18/62) among bacteriologically confirmed, and 30.8% (4/13) and 23.8% (5/21) among bacteriologically-negative participants. Among not TB patients, the specificity was 80.9% (123/152), being 78.3% (18/23) among samples stored less than 30 days and 81.4% (105/129) among samples stored for more than 30 days (p = 0.46). The detection of M. tuberculosis in oral mucosa samples is feasible, but storage conditions may affect the yield.

scholarly journals Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan

Data in Brief ◽  
2020 ◽  
Vol 33 ◽  
pp. 106416
Author(s):  
Asset Daniyarov ◽  
Askhat Molkenov ◽  
Saule Rakhimova ◽  
Ainur Akhmetova ◽  
Zhannur Nurkina ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data
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