Langille M.G.I.,Dalhousie University |
Laird M.R.,Simon Fraser University |
Hsiao W.W.L.,BCCDC Public Health Microbiology and Reference Laboratory |
Chiu T.A.,Simon Fraser University |
And 2 more authors.
Bioinformatics | Year: 2012
Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources. MicrobeDB provides a foundation for such projects by the automation of downloading published, completed bacterial and archaeal genomes from key sources, parsing annotations of all genomes (both public and private) into a local database, and allowing interaction with the database through an easy to use programming interface. MicrobeDB creates a simple to use, easy to maintain, centralized local resource for various large-scale comparative genomic analyses and a back-end for future microbial application design. © The Author(s) 2012. Published by Oxford University Press.
Mattison K.,Bureau of Microbial Hazards |
Grudeski E.,Public Health Agency of Canada |
Auk B.,BCCDC Public Health Microbiology and Reference Laboratory |
Brassard J.,Agriculture and Agri Food Canada |
And 18 more authors.
Journal of Clinical Virology | Year: 2011
Background: Noroviruses (NoVs) are the leading cause of infectious gastroenteritis worldwide. Real-time reverse transcription PCR (real-time RT-PCR) is the preferred method of NoV detection for the majority of testing laboratories. Although the accepted target region for molecular detection assays is the conserved ORF1/ORF2 junction, multiple variations have been published with differences in primers, probes, reagents, multiplexing, etc. Objectives: We assessed the detection limit for GII.4 NoV real-time RT-PCR assays as well as the ability to detect the non-GII.4 NoV genotypes in each participating laboratory. Study design: A panel of 25 RNA samples was circulated to 18 testing laboratories for comparison of their real-time RT-PCR procedures for NoV detection. Results: Multiple protocols with slight differences in reagents or conditions successfully detected 10 genome equivalents or fewer of NoV per reaction. Multiplex procedures were significantly associated (p= 0.04) with false negative results, particularly for a GI.2 strain. Sensitive detection was associated with false positive results (p= 0.03). Conclusions: Overall, the data indicate that comparable results are produced under slightly different assay conditions. © 2010.
Chu H.-T.,Asia University, Taiwan |
Hsiao W.W.L.,BCCDC Public Health Microbiology and Reference Laboratory |
Hsiao W.W.L.,University of British Columbia |
Chen J.-C.,Institute of Biotechnology |
And 11 more authors.
Bioinformatics | Year: 2013
Motivation: High-accuracy de novo assembly of the short sequencing reads from RNA-Seq technology is very challenging. We introduce a de novo assembly algorithm, EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo. This algorithm uses an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in RNA-Seq data.Results: EBARDenovo resolves the complications of RNA-Seq assembly arising from sequencing errors, repetitive sequences and aberrant chimeric amplicons. In a series of assembly experiments, our algorithm is the most accurate among the examined programs, including de Bruijn graph assemblers, Trinity and Oases. © 2013 The Author.
Sahni V.,Center for Disease Control |
Naus M.,Center for Disease Control |
Hoang L.,BCCDC Public Health Microbiology and Reference Laboratory |
Tyrrell G.J.,Provincial Laboratory for Public Health |
And 3 more authors.
Canadian Journal of Public Health | Year: 2012
Objectives: In 2003, British Columbia (BC) introduced a universal heptavalent pneumococcal conjugate vaccine (PCV-7) program for infants, and in 2007 revised the recommended schedule from four doses to three doses. We describe trends in the incidence of invasive pneumococcal disease (IPD) in association with these program changes. Methods: All confirmed cases are reported to the BC Centre for Disease Control (BCCDC) using a standardized data collection process; isolates are forwarded to the BCCDC Public Health and Reference Microbiology Laboratory for serotyping and to the National Reference Laboratory for confirmation. Upon implementation of the reduced dose program in 2007, additional epidemiological data, including immunization history, were collected for children ≤16 years. Results: Seven years after implementation of the program, a 78% decline in incidence of IPD among children under five has been achieved; this is largely a direct effect of the PCV-7 program. Among those >16 years of age, herd immunity is evident and decreasing trends of PCV-7 serotypes continued even after the dose reduction program was introduced. However, gains in disease reduction were offset by increases in replacement serotypes, particularly among the over-65 age group. This has resulted in no net change in adult IPD rates. Conclusions: The implementation of the PCV-7 program has changed the epidemiology of IPD in BC through direct effects of the vaccine, herd immunity and serotype replacement. The introduction of a three-dose schedule was not associated with an excess of vaccine failures. © Canadian Public Health Association, 2012.
Taylor D.,British Columbia Center for Disease Control |
Taylor D.,University of British Columbia |
Durigon M.,British Columbia Center for Disease Control |
Davis H.,Alberta Health Services |
And 13 more authors.
International Journal of STD and AIDS | Year: 2015
Failure to understand the risk of false-negative HIV test results during the window period results in anxiety. Patients typically want accurate test results as soon as possible while clinicians prefer to wait until the probability of a false-negative is virtually nil. This review summarizes the median window periods for third-generation antibody and fourth-generation HIV tests and provides the probability of a false-negative result for various days post-exposure. Data were extracted from published seroconversion panels. A 10-day eclipse period was used to estimate days from infection to first detection of HIV RNA. Median (interquartile range) days to seroconversion were calculated and probabilities of a false-negative result at various time periods post-exposure are reported. The median (interquartile range) window period for third-generation tests was 22 days (19–25) and 18 days (16–24) for fourth-generation tests. The probability of a false-negative result is 0.01 at 80 days’ post-exposure for third-generation tests and at 42 days for fourth-generation tests. The table of probabilities of falsely-negative HIV test results may be useful during pre- and post-test HIV counselling to inform co-decision making regarding the ideal time to test for HIV. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.
Skowronski D.M.,British Columbia Center for Disease Control |
Skowronski D.M.,University of British Columbia |
Janjua N.Z.,British Columbia Center for Disease Control |
Janjua N.Z.,University of British Columbia |
And 6 more authors.
Clinical Infectious Diseases | Year: 2012
Background. Parental immunization has been recommended as a "cocoon" strategy to prevent serious pertussis outcomes in early infancy. We illustrate the high number needed to vaccinate (NNV) for this program based on recent epidemiologic data from the provinces of Québec and British Columbia (BC), Canada. Methods. Surveillance trends were summarized for the period 1990-2010. Hospitalization, intensive care unit (ICU) admission, and mortality data were compiled from 2000 to 2009. The proportion of infant pertussis attributed to a parent was estimated at 35%, explored up to 55%. Adult vaccine efficacy (VE) was estimated at 85%. The NNV was calculated as [2 parents/(parent-attributable infant risk × parent VE)]. To capture at least 1 recent cyclical peak, NNV was derived for the period 2005-2009 and explored for peak/trough years. Results. Substantial decline has occurred in pertussis incidence across all age groups including infants, reaching a 20-year nadir in 2010 in both provinces. For the period 2005-2009, the risk of infant hospitalization and ICU admission was 57 and 7, respectively, per 100 000 in Québec and 33 and 7, respectively, per 100 000 in BC. In both provinces the risk of infant pertussis-related death over that period was <0.5 per 100000. The NNV for parental immunization was at least 1 million to prevent 1 infant death, approximately 100 000 for ICU admission, and >10 000 for hospitalization. Conclusions. In the context of low pertussis incidence, the parental cocoon program is inefficient and resource intensive for the prevention of serious outcomes in early infancy. Regions contemplating the cocoon program should consider the NNV based on local epidemiology. © The Author 2011. Published by Oxford University Press on behalf of the Infectious.
Hoang L.M.N.,BCCDC Public Health Microbiology and Reference Laboratory |
Hoang L.M.N.,University of British Columbia |
Philips P.,University of British Columbia |
Galanis E.,British Columbia Center for Disease Control
Clinical Microbiology Newsletter | Year: 2011
Cryptococcus gattii emerged on Vancouver Island, British Columbia, Canada, in 1999. Subsequent spread to the Vancouver lower mainland, Washington state, and Oregon has been documented. Unlike classic Cryptococcus neoformans, which causes disease in immunosuppressed individuals, C. gattii tends to cause disease in essentially immunocompetent individuals. This article reviews the epidemiology, clinical presentation, diagnosis, and treatment of infections caused by this now endemic yeast in the Pacific Northwest. © 2011 Elsevier Inc.
Somily A.M.,King Saud University |
Morshed M.G.,BCCDC Public Health Microbiology and Reference Laboratory |
Morshed M.G.,University of British Columbia
Journal of Infection in Developing Countries | Year: 2015
Helicobacter pylori is a micro-aerophilic, slow-growing, Gram-negative spiral bacterium that colonizes the mucous lining of the human stomach. Infection with this bacterium has been identified as a cause of gastritis, peptic ulcer disease, and gastric mucosa-associated lymphoid tissue lymphoma. Globally, the prevalence of H. pylori-related infection is high compared to any other infectious diseases, and the rate of prevalence much higher in developing countries than in developed nations. This review article aims to describe the trend of H. pylori-related works in the Kingdom of Saudi Arabia (KSA) and the use of various laboratory tests for the diagnosis of H. pylori-related infections in adults and children. Therefore, published literature was referenced in the explanation and discussion of the different methods used to diagnose H. pylori-related disease, including papers published in the KSA and other Middle Eastern countries. The PubMed (http://www.ncbi.nlm.nih.gov/pubmed?cmd=search) search engine was used extensively. Culture and histopathology tests have been employed widely to detect this pathogen at the early stage. However, over the years, an array of tests including the rapid urease test, serology, the urea breath test, the fecal antigen test, and molecular testing have been developed to diagnose and better manage H. pylori-associated diseases since the discovery of this novel pathogen. © 2015 Somily et al.
Flaherty B.,University of British Columbia |
Pacheco-Vega R.,University of British Columbia |
Isaac-Renton J.,BCCDC Public Health Microbiology and Reference Laboratory
Water International | Year: 2011
Co-operative management of transboundary environmental resources is critical for peaceful relations between bordering nations. This article examines the current body of literature on Canada-United States transboundary water resources, specifically focusing this analysis on the level of attention given to (1) water quality vs. quantity and (2) groundwater vs. surface water concerns. These issues are discussed under the policy regime framework, examining the influence of institutions, interests and ideas on the relevant scholarly research and legislation. Canada-US transboundary water literature historically places more emphasis on water quantity and surface water issues. © Copyright 2011 International Water Resources Association.
Van Buynder P.G.,Fraser Health Authority and 400 |
Van Buynder P.G.,Simon Fraser University |
Van Buynder P.G.,University of Western Australia |
Konrad S.,Fraser Health Authority and 400 |
And 5 more authors.
Vaccine | Year: 2013
Background: Influenza is associated with a high mortality and morbidity in older adults. Vaccination remains the most effective method of preventing influenza and its consequences, however, vaccine effectiveness decreases with increasing age and increasing immunosenescence. In older adults, immunogenicity studies suggest an MF59 adjuvanted influenza vaccine (ATIV, Fluad®) may help. Methods: We evaluated the comparative effectiveness of ATIV, and unadjuvanted trivalent influenza vaccine (TIV) in reducing laboratory confirmed influenza in the elderly. Elderly in three health authorities during winter 2011-12 were included in a community based case control study design. Cases tested positive and controls tested negative for influenza. Subjects with known immunosuppression were excluded. Logistic regression was used to calculate the odds ratio of vaccination (vs. no vaccination) in cases and controls. ATIV and TIV effectiveness was described. Results: A total of 282 eligible participants were enrolled (84 cases). Almost half (136) were in a long term care facility and were 85 years of age or older (132) vaccine effectiveness decreased with increasing age. In a variety of multivariate analyses, ATIV was significantly protective at around 60% (p= 0.02), with only residence in long term care and health authority also significant. Vaccine effectiveness increased in non-long term care residents. In multivariate analyses TIV was ineffective. Conclusion: An MF59 adjuvanted vaccine provided significantly improved protection against influenza in the elderly. © 2013 The Authors.