A5012079379- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Algorithms and Data Compression
- Infectious Diseases and Tuberculosis
- Antibiotic Resistance in Bacteria
- Tracheal and airway disorders
- Microscopic Colitis
- Bariatric Surgery and Outcomes
- Obstructive Sleep Apnea Research
- Neuroscience of respiration and sleep
- Clostridium difficile and Clostridium perfringens research
- Bacterial Identification and Susceptibility Testing
- Pneumocystis jirovecii pneumonia detection and treatment
- Infectious Diseases and Mycology
- Enterobacteriaceae and Cronobacter Research
- HIV/AIDS Research and Interventions
- Advanced Malware Detection Techniques
- Obesity and Health Practices
- Cardiovascular Syncope and Autonomic Disorders
- Web Application Security Vulnerabilities
- Vibrio bacteria research studies
- Biomedical Text Mining and Ontologies
- Helicobacter pylori-related gastroenterology studies
University Hospital Heidelberg
2021
Heidelberg University
2021
University of Mendoza
2020
University of Oxford
2013-2017
Centre for Human Genetics
2016-2017
Roland Hill (United Kingdom)
2017
University College London
2017
John Radcliffe Hospital
2013-2015
National Institute for Health Research
2015
Oxford BioMedica (United Kingdom)
2013
ABSTRACT Routine full characterization of Mycobacterium tuberculosis is culture based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surveillance; such data could be transformative if provided at or near the point care. We demonstrate a low-cost method DNA extraction directly from patient samples M. WGS. initially evaluated by using Illumina MiSeq sequencer (40 smear-positive...
Whole-genome sequencing potentially represents a single, rapid and cost-effective approach to defining resistance mechanisms predicting phenotype, strain type, for both clinical epidemiological purposes. This retrospective study aimed determine the efficacy of whole genome-based antimicrobial prediction in isolates Escherichia coli Klebsiella pneumoniae. Seventy-four E. 69 K. pneumoniae bacteraemia from Oxfordshire, UK, were sequenced (Illumina HiSeq 2000). Resistance phenotypes predicted...
BackgroundSlow and cumbersome laboratory diagnostics for Mycobacterium tuberculosis complex (MTBC) risk delayed treatment poor patient outcomes. Whole-genome sequencing (WGS) could potentially provide a rapid comprehensive diagnostic solution. In this prospective study, we compare real-time WGS with routine MTBC workflows.MethodsWe compared mycobacteria from all newly positive liquid cultures workflows across eight laboratories in Europe North America accuracy, processing times, cost between...
The control of Clostridium difficile infections is an international clinical challenge. incidence C in England declined by roughly 80% after 2006, following the implementation national policies; we tested two hypotheses to investigate their role this decline. First, if infection declines were driven reductions use particular antibiotics, then caused resistant isolates should decline faster than that susceptible across multiple genotypes. Second, improvements hospital control, transmitted...
BackgroundPatients born outside the UK have contributed to a 20% rise in UK's tuberculosis incidence since 2000, but their effect on domestic transmission is not known. Here we use whole-genome sequencing investigate epidemiology of an unselected population over 6 years.MethodsWe identified all residents with Oxfordshire postcodes Mycobacterium culture or clinical diagnosis between Jan 1, 2007, and Dec 31, 2012, using local databases checking against national Enhanced Tuberculosis...
An urgent UK investigation was launched to assess risk of invasive Mycobacterium chimaera infection in cardiothoracic surgery and a possible association with cardiopulmonary bypass heater-cooler units following alerts Switzerland The Netherlands.Parallel investigations were pursued: (1) identification bypass-associated M. through national laboratory hospital admissions data linkage; (2) cohort study patient risk; (3) microbiological aerobiological heater-coolers situ under controlled...
ABSTRACT We developed a low-cost and reliable method of DNA extraction from as little 1 ml early positive mycobacterial growth indicator tube (MGIT) cultures that is suitable for whole-genome sequencing to identify species predict antibiotic resistance in clinical samples. The based on ethanol precipitation supplemented by pretreatment steps with MolYsis kit or saline wash the removal human final cleanup step solid-phase reversible immobilization beads. protocol yielded ≥0.2 ng/μl 90%...
ABSTRACT Use of whole-genome sequencing (WGS) for routine mycobacterial species identification and drug susceptibility testing (DST) is becoming a reality. We compared the performances WGS standard laboratory workflows prospectively, by parallel processing at major reference service over course 1 year, identification, first-line Mycobacterium tuberculosis resistance prediction, turnaround time. Among 2,039 isolates with line probe assay results 74 (3.6%) failed or identification. Excluding...
Abstract Objectives Intestinal carriage constitutes an important reservoir of antimicrobial-resistant bacteria, with some the highest rates reported from Asia. Antibiotic resistance has been little studied in Laos, where antibiotics are available without restriction, but others such as carbapenems not available. Patients and methods We collected stools 397 healthy children 12 randomly selected pre-school childcare facilities around Vientiane. Colonization ESBL-producing Enterobacteriaceae...
Whole-genome sequencing was used to determine whether the reductions in recurrence of Clostridium difficile infection observed with fidaxomicin pivotal phase 3 trials occurred by preventing relapse same infection, reinfection a new strain, or both outcomes. Paired isolates C. were available from 93 199 participants recurrences (28 treated fidaxomicin, and 65 vancomycin). Given evolutionary rates, paired samples ≤2 single-nucleotide variants (SNVs) apart considered relapses, >10 SNVs...
Abstract Routine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surveillance; such data could be transformative if provided at or near point care. We demonstrate a low-cost DNA extraction method TB WGS direct from patient samples. initially evaluated the using Illumina MiSeq sequencer (40 smear-positive...
Abstract We show how positional markers can be used to encode genetic variation within aBurrows-Wheeler Transform (BWT), and use this construct a generalisation ofthe traditional “reference genome”, incorporating known aspecies. Our goal is support the inference of closest mosaic previouslyknown sequences genome(s) under analysis. scheme results in an increased alphabet size, by using wavelet tree encoding BWT we reduce performance impact on rank operations. give specialised form backward...
The usefulness of pulse oximetry for the management obstructive sleep apnea is controversial. aim this study was to assess accuracy indication Continuous Positive Airway Pressure (CPAP) treatment in patients with suspected (OSA) based on clinical and data as compared polysomnography (PSG).This multicenter observational involved seven laboratories. Patients suspicion OSA who completed a standardized questionnaire diagnostic PSG were enrolled. Eight observers logged website independently...
A Web browser is probably the main attack vector used by hackers. Solutions to browser's security are difficult foresee, due influence of user-behaviour. In this paper, we show how tackle issue securing web browsers introducing a Secure Cloud Browser (SCB) architecture. The rationale behind SCB reduce vulnerability transporting it remote secure environment, making ephemeral and renovating in manner that transparent user. Our scheme allows user browse application while source code remotely...