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Dooley D.M.,University of British Columbia | Petkau A.J.,Public Health Agency of Canada | Van Domselaar G.,Public Health Agency of Canada | Hsiao W.W.L.,University of British Columbia | Hsiao W.W.L.,BC Public Health Microbiology and Reference Laboratory
Bioinformatics | Year: 2016

Motivation: There are various reasons for rerunning bioinformatics tools and pipelines on sequencing data, including reproducing a past result, validation of a new tool or workflow using a known dataset, or tracking the impact of database changes. For identical results to be achieved, regularly updated reference sequence databases must be versioned and archived. Database administrators have tried to fill the requirements by supplying users with one-off versions of databases, but these are time consuming to set up and are inconsistent across resources. Disk storage and data backup performance has also discouraged maintaining multiple versions of databases since databases such as NCBI nr can consume 50 Gb or more disk space per version, with growth rates that parallel Moore's law. Results: Our end-to-end solution combines our own Kipper software package-a simple key-value large file versioning system-with BioMAJ (software for downloading sequence databases), and Galaxy (a web-based bioinformatics data processing platform). Available versions of databases can be recalled and used by command-line and Galaxy users. The Kipper data store format makes publishing curated FASTA databases convenient since in most cases it can store a range of versions into a file marginally larger than the size of the latest version. © 2015 The Author.


Henrich N.,Providence Health Care Research Institute | Holmes B.,Michael Smith Foundation for Health Research | Prystajecky N.,BC Public Health Microbiology and Reference Laboratory | Prystajecky N.,University of British Columbia
PLoS ONE | Year: 2015

In association with the development of new microbial tests for source water quality (SWQ), focus groups with members of the public were conducted to gain insight into their perceptions of SWQ, behaviours and contaminants they think pose the greatest threat to its quality, and what/how they want to know about SWQ. Discussions revealed a low concern about SWQ in general, and in particular about microbial contamination. Participants identified behaviours that threaten SWQ, barriers to changing behaviour and suggestions for inducing change. A strong desire was expressed for water quality information to be interpreted and communicated in terms of how SWQ may impact human health and how their actions should be altered in response to test results. The information can be used to inform communication strategies and possibly impact policies associated with water quality testing and implementation of new tests. More broadly, awareness of the public’s understanding and beliefs about source water can be used in working with the public to adopt water-friendly behaviours, influence the content and methods of communicating with the public about water issues and water quality, and could contribute to the direction of future research and investment into water technologies to align with the public's priorities. © 2015 Henrich et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Tsang R.S.W.,Public Health Agency of Canada | Hoang L.,BC Public Health Microbiology and Reference Laboratory | Tyrrell G.,Provincial Laboratory for Public Health | Horsman G.,Saskatchewan Disease Control Laboratory | And 5 more authors.
Journal of Medical Microbiology | Year: 2015

We previously reported a shift in the electrophoretic type (ET) of invasive MenC in Canada from predominantly ET-15 to ET-37 in the post-MenC conjugate vaccine period. This study sought to confirm this trend by examining all culture-confirmed invasive MenC case isolates in Canada in the period from 1 January 2009 to 31 December 2013. Of the 50 MenC isolates, 18 belonged to ET-15, 28 belonged to ET-37 (but not ET-15), and four belonged to other clonal types. Analysis of the serotype and serosubtype antigens, porA and fetA gene sequences provided data to show that invasive MenC belonging to ET-15 and ET-37 were two very different subpopulations within the ST-11 clonal complex. Sequence analysis of the fHbp genes suggested that 12 different types of factor H-binding protein were found among the ET-15 isolates while 86% of ET-37 isolates were found to have fHbp genes predicted to encode peptide 22. The nadA gene in 12 MenC isolates was disrupted due to IS1301 insertion and 11 of these 12 isolates belonged to ET-15. Ten per cent of the invasive MenC were found to have a frame-shift mutation in their fHbp genes that predicted no fHbp produced. Significant diversity and frame-shift mutations of fHbp genes were found in invasive MenC strains in Canada. © 2015 The Authors.


Taylor M.,British Columbia Center for Disease Control | McIntyre L.,British Columbia Center for Disease Control | Ritson M.,Vancouver Coastal Health Authority | Stone J.,Fraser Health Authority | And 12 more authors.
Marine Drugs | Year: 2013

In 2011, a Diarrhetic Shellfish Poisoning (DSP) outbreak occurred in British Columbia (BC), Canada that was associated with cooked mussel consumption. This is the first reported DSP outbreak in BC. Investigation of ill individuals, traceback of product and laboratory testing for toxins were used in this investigation. Sixty-two illnesses were reported. Public health and food safety investigation identified a common food source and harvest area. Public health and regulatory agencies took actions to recall product and notify the public. Shellfish monitoring program changes were implemented after the outbreak. Improved response and understanding of toxin production will improve management of future DSP outbreaks. © 2013 by the authors; licensee MDPI.


Lunny C.,Center for Disease Control | Lunny C.,University of British Columbia | Lunny C.,Monash University | Taylor D.,Center for Disease Control | And 15 more authors.
PLoS ONE | Year: 2015

Background: The increases in STI rates since the late 1990s in Canada have occurred despite widespread primary care and targeted public health programs and in the setting of universal health care. More innovative interventions are required that would eliminate barriers to STI testing such as internet-based or mail-in home and community service testing for patients that are hard to reach, who refuse to go for clinician-based testing, or who decline an examination. Jurisdictions such as New Zealand and some American states currently use self-collected sampling, but without the required evidence to determine whether self-collected specimens are as accurate as clinician-collected specimens in terms of chlamydia and gonorrhea diagnostic accuracy. The objective of the review is to compare self-collected vaginal, urine, pharyngeal and rectal samples to our reference standard - clinician-collected cervical, urethral, pharyngeal and rectal sampling techniques to identify a positive specimen using nucleic acid amplification test assays. Methods: The hierarchical summary receiver operating characteristic and the fixed effect models were used to assess the accuracy of comparable specimens that were collected by patients compared to clinicians. Sensitivity and specificity estimates with 95% confidence intervals (CI) were reported as our main outcome measures. Findings: We included 21 studies based on over 6100 paired samples. Fourteen included studies examined chlamydia only, 6 compared both gonorrhea and chlamydia separately in the same study, and one examined gonorrhea. The six chlamydia studies comparing self-collection by vaginal swab to a clinician-collected cervical swab had the highest sensitivity (92%, 95% CI 87-95) and specificity (98%, 95% CI 97-99), compared to other specimen-types (urine/urethra or urine/cervix). Six studies compared urine self-samples to urethra clinician-collected samples in males and produced a sensitivity of 88% (95% CI 83-93) and a specificity of 99% (95% CI 0.94-0.99). Taking into account that urine samples may be less sensitive than cervical samples, eight chlamydia studies that compared urine self-collected verses clinician-collected cervical samples had a sensitivity of 87% (95% CI 81-91) and high specificity of 99% (95% CI 0.98-1.00). For gonorrhea testing, self-collected urine samples compared to clinician-collected urethra samples in males produced a sensitivity of 92% (95% CI 83-97) and specificity of 99% (95% CI 0.98-1.00). Conclusion: The sensitivity and specificity of vaginal self-collected swabs compared to swabs collected by clinicians supports the use of vaginal swab as the recommended specimen of choice in home-based screening for chlamydia and gonorrhea. Urine samples for gonorrhea collected by men had comparably high sensitivity and specificity, so could be recommended as they can be left at room temperature for several days, allowing for the possibility of mailin home-based testing. In populations that may not go for testing at all, do not have the option of clinical testing, or who refuse a clinical examination, self-collected screening would be a good alternative. We recommend that guidelines on how to self-collect gonorrhea and chlamydia urine, vaginal, rectal and pharyngeal specimens be published. © 2015 Lunny et al.

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