Clinical use of Whole Genome Sequencing for Mycobacterium tuberculosis

Drug resistant tuberculosis (TB) remains a major challenge to global health and to healthcare in the UK. In 2014, England recorded 6520 cases of TB of which 1.4% were multi-drug resistant (MDR-TB). Extensively drug resistant TB (XDR-TB) occurs at a much lower rate, but the impact on the patient and hospital is severe. Current diagnostic methods such as drug susceptibility testing and targeted molecular tests are slow to return or examine only a limited number of target regions respectively. Faster, more comprehensive diagnostics will enable earlier use of the most appropriate drug regimen thus improving patient outcome and reducing overall healthcare costs. Whole genome sequencing has been shown to provide a rapid and comprehensive view of the genotype of the organism and thus enable reliable prediction of the drug susceptibility phenotype within a clinically relevant time frame. In addition it provides the highest resolution when investigating transmission events in possible outbreak scenarios. However, robust software and database tools need to be developed for the full potential to be realized in this specialized area of medicine

Evaluation of Xpert® MTB/RIF and ustar easyNAT™ TB IAD for diagnosis of tuberculous lymphadenitis of children in Tanzania : a prospective descriptive study

Fine needle aspiration biopsy has become a standard approach for diagnosis of peripheral tuberculous lymphadenitis. The aim of this study was to compare the performance of Xpert MTB/RIF and Ustar EasyNAT TB IAD nucleic acid amplification assays, against acid-fast bacilli microscopy, cytology and mycobacterial culture for the diagnosis of TB lymphadenitis in children from a TB-endemic setting in Tanzania.; Children of 8 weeks to 16 years of age, suspected of having TB lymphadenitis, were recruited at a district hospital in Tanzania. Fine needle aspirates of lymph nodes were analysed using acid-fast bacilli microscopy, liquid TB culture, cytology, Xpert MTB/RIF and EasyNAT. Latent class analysis and comparison against a composite reference standard comprising "culture and/or cytology" was done, to assess the performance of Xpert MTB/RIF and EasyNAT for the diagnosis of TB lymphadenitis.; Seventy-nine children were recruited; 4 were excluded from analysis. Against a composite reference standard of culture and/or cytology, Xpert MTB/RIF and EasyNAT had a sensitivity and specificity of 58 % and 93 %; and 19 % and 100 % respectively. Relative to latent class definitions, cytology had a sensitivity of 100 % and specificity of 94.7 %.; Combining clinical assessment, cytology and Xpert MTB/RIF may allow for a rapid and accurate diagnosis of childhood TB lymphadenitis. Larger diagnostic evaluation studies are recommended to validate these findings and on Xpert MTB/RIF to assess its use as a solitary initial test for TB lymphadenitis in children

A Competence-based Service for Supporting Self-Regulated Learning in Virtual Environments

This  paper  presents  a  conceptual  approach  and  a  Web-based  service  that  aim  at  supporting self-regulated learning in virtual environments. The conceptual approach consists of four  components:  1)  a  self-regulated  learning  model  for  supporting  a  learner-centred  learning  process, 2) a psychological model for facilitating competence-based personalization and knowledge assessment, 3) an open learner model approach for visual interaction and feedback, and 4) a learning analytics approach for capturing relevant learner information required by the other  components.  The  Web-based  service  provides  a  technical  implementation  of  the  conceptual approach, as well as a linkage to existing virtual environments used for learning purposes. The approach and service have been evaluated in user studies in university courses on computer  science  to  demonstrate  the  usefulness  of  the  overall  approach  and  to  get  an  understanding of some limitations

Tuberculosis diagnostics and biomarkers: needs, challenges, recent advances, and opportunities

Tuberculosis is unique among the major infectious diseases in that it lacks accurate rapid point-of-care diagnostic tests. Failure to control the spread of tuberculosis is largely due to our inability to detect and treat all infectious cases of pulmonary tuberculosis in a timely fashion, allowing continued Mycobacterium tuberculosis transmission within communities. Currently recommended gold-standard diagnostic tests for tuberculosis are laboratory based, and multiple investigations may be necessary over a period of weeks or months before a diagnosis is made. Several new diagnostic tests have recently become available for detecting active tuberculosis disease, screening for latent M. tuberculosis infection, and identifying drug-resistant strains of M. tuberculosis. However, progress toward a robust point-of-care test has been limited, and novel biomarker discovery remains challenging. In the absence of effective prevention strategies, high rates of early case detection and subsequent cure are required for global tuberculosis control. Early case detection is dependent on test accuracy, accessibility, cost, and complexity, but also depends on the political will and funder investment to deliver optimal, sustainable care to those worst affected by the tuberculosis and human immunodeficiency virus epidemics. This review highlights unanswered questions, challenges, recent advances, unresolved operational and technical issues, needs, and opportunities related to tuberculosis diagnostics

Characterization of Nanoparticle Release from Surface Coatings by the Simulation of a Sanding Process

Nanoparticles are used in industrial and domestic applications to control customized product properties. But there are several uncertainties concerning possible hazard to health safety and environment. Hence, it is necessary to search for methods to analyze the particle release from typical application processes. Based on a survey of commercial sanding machines, the relevant sanding process parameters were employed for the design of a miniature sanding test setup in a particle-free environment for the quantification of the nanoparticle release into air from surface coatings. The released particles were moved by a defined airflow to a fast mobility particle sizer and other aerosol measurement equipment to enable the determination of released particle numbers additionally to the particle size distribution. First, results revealed a strong impact of the coating material on the swarf mass and the number of released particles

Home Is Where the Smart Is: Development and Validation of the Cybersecurity Self-Efficacy in Smart Homes (CySESH) Scale

The ubiquity of devices connected to the internet raises concerns about the security and privacy of smart homes. The effectiveness of interventions to support secure user behaviors is limited by a lack of validated instruments to measure relevant psychological constructs, such as self-efficacy - the belief that one is able to perform certain behaviors. We developed and validated the Cybersecurity Self-Efficacy in Smart Homes (CySESH) scale, a 12-item unidimensional measure of domain-specific self-efficacy beliefs, across five studies (N = 1247). Three pilot studies generated and refined an item pool. We report evidence from one initial and one major, preregistered validation study for (1) excellent reliability (α = 0.90), (2) convergent validity with self-efficacy in information security (rSEIS = 0.64, p < .001), and (3) discriminant validity with outcome expectations (rOE = 0.26, p < .001), self-esteem (rRSE = 0.17, p < .001), and optimism (rLOT-R = 0.18, p < .001). We discuss CySESH's potential to advance future HCI research on cybersecurity, practitioner user assessments, and implications for consumer protection policy

Home Is Where the Smart Is: Development and Validation of the Cybersecurity Self-Efficacy in Smart Homes (CySESH) Scale

The ubiquity of devices connected to the internet raises concerns about the security and privacy of smart homes. The effectiveness of interventions to support secure user behaviors is limited by a lack of validated instruments to measure relevant psychological constructs, such as self-efficacy – the belief that one is able to perform certain behaviors. We developed and validated the Cybersecurity Self-Efficacy in Smart Homes (CySESH) scale, a 12-item unidimensional measure of domain-specific self-efficacy beliefs, across five studies (N = 1247). Three pilot studies generated and refined an item pool. We report evidence from one initial and one major, preregistered validation study for (1) excellent reliability (α = 0.90), (2) convergent validity with self-efficacy in information security (rSEIS = 0.64, p < .001), and (3) discriminant validity with outcome expectations (rOE = 0.26, p < .001), self-esteem (rRSE = 0.17, p < .001), and optimism (rLOT-R = 0.18, p < .001). We discuss CySESH’s potential to advance future HCI research on cybersecurity, practitioner user assessments, and implications for consumer protection policy

The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa

Background. The Beijing genotype of M. tuberculosis is a virulent strain that is disseminating worldwide and has a strong association with drug resistance. In the Western Cape of South Africa, epidemiological studies have identified the R220 cluster of the Beijing genotype as a major contributor to a recent outbreak of drug-resistant tuberculosis. Although the outbreak is considered to be due to clonal transmission, the relationship among drug resistant isolates has not yet been established. Results. To better understand the evolution of drug resistance among these strains, 14 drug-resistant clinical isolates of the Beijing genotype were sequenced by whole-genome sequencing, including eight from R220 and six from a more ancestral Beijing cluster, R86, for comparison. While each cluster shares a distinct resistance mutation for isoniazid, mapping of other drug-resistance mutations onto a phylogenetic tree constructed from single nucleotide polymorphisms shows that resistance mutations to many drugs have arisen multiple times independently within each cluster of isolates. Thus, drug resistance among these isolates appears to be acquired, not clonally derived. This observation suggests that, although the Beijing genotype as a whole might have selective advantages enabling its rapid dissemination, the XDR isolates are relatively less fit and do not propagate well. Although it has been hypothesized that the increased frequency of drug resistance in some Beijing lineages might be caused by a mutator phenotype, no significant shift in synonymous substitution patterns is observed in the genomes. Conclusion. While MDR-TB is spreading by transmission in the Western Cape, our data suggests that further drug resistance (i.e. XDR-TB) at this stage is acquired.Peer Reviewe

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online ‘TB-Profiler’ tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing

Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip

The emergence of pathogens resistant to existing antimicrobial drugs is a growing worldwide health crisis that threatens a return to the pre-antibiotic era. To decrease the overuse of antibiotics, molecular diagnostics systems are needed that can rapidly identify pathogens in a clinical sample and determine the presence of mutations that confer drug resistance at the point of care. We developed a fully integrated, miniaturized semiconductor biochip and closed-tube detection chemistry that performs multiplex nucleic acid amplification and sequence analysis. The approach had a high dynamic range of quantification of microbial load and was able to perform comprehensive mutation analysis on up to 1,000 sequences or strands simultaneously in <2 h. We detected and quantified multiple DNA and RNA respiratory viruses in clinical samples with complete concordance to a commercially available test. We also identified 54 drug-resistance-associated mutations that were present in six genes of Mycobacterium tuberculosis, all of which were confirmed by next-generation sequencing