A5102862234- Antimicrobial Resistance in Staphylococcus
- Bacterial Identification and Susceptibility Testing
- Fibromyalgia and Chronic Fatigue Syndrome Research
- Bacterial biofilms and quorum sensing
- Streptococcal Infections and Treatments
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Mycobacterium research and diagnosis
- Exercise and Physiological Responses
- Infective Endocarditis Diagnosis and Management
- Microbial Metabolism and Applications
- Viral Infections and Immunology Research
- Genetic factors in colorectal cancer
- RNA and protein synthesis mechanisms
- Clostridium difficile and Clostridium perfringens research
- Healthcare Systems and Public Health
- Cystic Fibrosis Research Advances
- Genetic Associations and Epidemiology
- Eosinophilic Disorders and Syndromes
- Cancer Cells and Metastasis
- Escherichia coli research studies
- Nasal Surgery and Airway Studies
- bioluminescence and chemiluminescence research
- Muscle Physiology and Disorders
- Genetic Neurodegenerative Diseases
University of British Columbia
2013-2022
John Radcliffe Hospital
2008-2021
University of Oxford
2008-2021
Pfizer (Germany)
2020
Washington University in St. Louis
2016
BC Centre for Disease Control
2014-2015
Ministry of Agriculture
2014
National Institute for Health Research
2013
Whole-genome sequencing offers new insights into the evolution of bacterial pathogens and etiology disease. Staphylococcus aureus is a major cause bacteria-associated mortality invasive disease carried asymptomatically by 27% adults. Eighty percent bacteremias match strain. However, role evolutionary change in pathogen during progression from carriage to incompletely understood. Here we use high-throughput genome discover genetic changes that accompany transition nasal fatal bloodstream...
Staphylococcus aureus is a major cause of healthcare associated mortality, but like many important bacterial pathogens, it common constituent the normal human body flora. Around third healthy adults are carriers. Recent evidence suggests that evolution S. during nasal carriage may be with progression to invasive disease. However, more detailed understanding within-host under natural conditions required appreciate evolutionary and mechanistic reasons why commensal bacteria such as Therefore...
Abstract Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome clonal species, including major pathogen Staphylococcus aureus , incompletely understood. Here we reveal widespread homologous recombination S. at species level, contrast to its near-complete absence between closely related strains. We discover a patchwork hotspots and coldspots fine scales falling against backdrop broad-scale trends rate variation. Over megabases,...
Abstract Circulating tumour DNA (ctDNA) detection via liquid biopsy is an emerging alternative to tissue biopsy, but its potential in treatment response monitoring and prognosis triple negative breast cancer (TNBC) not yet well understood. Here we determined the prevalence of actionable mutations detectable ctDNA using a clinically validated gene panel assay patients with TNBC, without recurrence at time study entry. Sequencing plasma validation variants from 130 TNBC collected within 7...
Staphylococcal protein A (spa) is an important virulence factor which enables Staphylococcus aureus to evade host immune responses. Genotypes known as "spa-types", based on highly variable Xr region sequences of the spa-gene, are frequently used classify strains. weakness current spa-typing primers that rearrangements in IgG-binding gene cause 1-2% strains be designated "non-typeable".We developed improved primer enabled sequencing all strains, containing any type genetic rearrangement, a...
Giardia causes the diarrheal disease known as giardiasis; transmission through contaminated surface water is common. The protozoan parasite's genetic diversity has major implications for human health and epidemiology. To determine extent of from wildlife water, we performed whole-genome sequencing (WGS) to characterize 89 duodenalis isolates both outbreak sporadic infections: 29 raw 38 humans, 22 veterinary sources. Using single nucleotide variants (SNVs), combined with epidemiological data,...
Genomic analysis of cancer tissues is an essential aspect personalized oncology treatment. Though it has been suggested that formalin fixation patient may be suboptimal for molecular studies, this tissue processing approach remains the industry standard. Therefore clinical laboratories must able to work with fixed, paraffin embedded (FFPE) material. This study examines effects pre-analytic variables introduced by routine pathology on specimens used reports produced next-generation sequencing...
Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of multi-drug-resistant infections in people, particularly indigent populations. MRSA can be transmitted between people and domestic animals, but the potential for transmission commensal pests, rodents, had not been investigated. The objective this study was to identify presence characterize ecology rats (Rattus spp.) from impoverished, inner-city neighborhood. Oropharyngeal swabs were collected trapped 33 city blocks...
Background In the past, strains of Staphylococcus aureus have evolved, expanded, made a marked clinical impact and then disappeared over several years. Faced with rising meticillin-resistant S (MRSA) rates, UK government-supported infection control interventions were rolled out in Oxford Radcliffe Hospitals NHS Trust from 2006 onwards. Methods Using an electronic Database, authors identified isolation MRS among 611 434 hospital inpatients admitted to acute hospitals Oxford, UK, 1 April 1998...
Staphylococcus aureus is a commensal that can also cause invasive infection. Reports suggest nasal cocolonization occurs rarely, but the resources required to sequence multiple colonies have precluded its large-scale investigation. A staged protocol was developed maximize detection of mixed-spa-type colonization while minimizing laboratory using 3,197 S. aureus-positive samples from longitudinal study healthy individuals in Oxfordshire, United Kingdom. Initial typing pooled material each...
Staphylococcus aureus nasal carriage increases infection risk. However, few studies have investigated S. acquisition/loss over >1 year, and fewer still used molecular typing.1123 adults attending five Oxfordshire general practices had swabs taken. 571 were re-swabbed after one month then every two months for median years. All isolates spa-typed. Risk factors collected from interviews medical records.32% carried at recruitment (<1% MRSA). Rates of spa-type acquisition similar in participants...
A subset of patients reporting a diagnosis Lyme disease can be described as having alternatively diagnosed chronic syndrome (ADCLS), in which is based on laboratory results from nonreference specialty using in-house criteria. Patients with ADCLS report symptoms similar to those reported by fatigue (CFS).We performed case-control study comparing and CFS each other both healthy controls systemic lupus erythematosus (SLE). Subjects completed history, physical exam, screening tests, 7 functional...
Myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) is a of unknown etiology characterized by profound exacerbated physical activity, also known as post-exertional malaise (PEM). Previously, we did not detect evidence immune dysregulation or virus reactivation outside PEM periods. Here sought to determine whether cardiopulmonary exercise stress testing ME/CFS patients could trigger such changes. (n = 14) and matched sedentary controls 11) were subjected on 2 consecutive days...
Abstract As metagenomic approaches for detecting infectious agents have improved, each tissue that was once thought to be sterile has been found harbor a variety of microorganisms. Controversy still exists over the status amniotic fluid, which is part an immunologically privileged zone required prevent maternal immune system rejection fetus. Due this privilege, exclusion microbes proposed mandatory, leading womb hypothesis. Since nucleic acid yields from fluid are very low, contaminating in...
New strains of meticillin-resistant Staphylococcus aureus (MRSA) may be associated with changes in rates disease or clinical presentation. Conventional typing techniques not detect new clonal variants that underlie epidemiology phenotype.To investigate the role MRSA an outbreak bacteraemia at a hospital England.Bacteraemia isolates major UK lineages (EMRSA-15 and -16) from before after were analysed by whole-genome sequencing context epidemiological data. For comparison, EMRSA-15 -16 another...
Carriage of Staphylococcus aureus is a risk for infections. Targeted decolonization reduces postoperative infections but depends on accurate screening.To compare detection S. carriage in healthy individuals between anatomical sites and nurse- versus self-swabbing; also to determine whether single nasal swab predicted over four weeks.Healthy were recruited via general practices. After consent, nurses performed multi-site swabbing (nose, throat, axilla). Participants twice-weekly weeks. Swabs...
is a major bacterial pathogen in humans, and dominant cause of severe bloodstream infections. Globally, antimicrobial resistance (AMR)
Chronic fatigue syndrome (CFS) remains poorly understood. Although infections are speculated to trigger the syndrome, a specific infectious agent and underlying pathophysiological mechanism remain elusive. In previous study, we described similar clinical phenotypes in CFS patients alternatively diagnosed chronic Lyme (ADCLS) patients—individuals with disease by testing from private specialty laboratories but who test negative reference 2-tiered serologic analysis.
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating disease causing indefinite fatigue. ME/CFS has long been hypothesised to have an infectious cause; however, no specific agent identified. We used metagenomics analyse the RNA from plasma samples 25 individuals with and compare their microbial content technical controls as well three control groups: alternatively diagnosed chronic Lyme syndrome (N = 13), systemic lupus erythematosus 11), healthy 25). found that...
Inuit are the Indigenous Arctic peoples and residents of Canadian territory Nunavut who have highest global rate lung cancer. Given cancer's mortality, histological genomic characterization was undertaken to better understand disease biology. We retrospectively studied all cases from Nunavut's Qikiqtani (Baffin) region, referred Ottawa Hospital Cancer Center between 2001 2011. Demographics were compiled medical records tumor samples underwent pathologic/histologic confirmation. Tumors...
Burkholderia cepacia complex bacteria are amongst the most feared of pathogens in cystic fibrosis (CF). The BCC comprises at least 20 distinct species that can cause chronic and unpredictable lung infections CF. Historically B. cenocepacia has been prevalent CF associated some centers with high rates mortality. Modeling infection by laboratory is challenging no models exist which effectively recapitulate disease caused bacteria. Therefore our understanding factors contribute towards...