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Adamiak P.,Immunology and Infectious Diseases | Vanderkooi O.G.,Immunology and Infectious Diseases | Vanderkooi O.G.,University of Calgary | Vanderkooi O.G.,535 Research Rd Nw | And 6 more authors.
BMC Microbiology

Background: Multi-locus sequence typing (MLST) is a portable, broadly applicable method for classifying bacterial isolates at an intra-species level. This methodology provides clinical and scientific investigators with a standardized means of monitoring evolution within bacterial populations. MLST uses the DNA sequences from a set of genes such that each unique combination of sequences defines an isolate's sequence type. In order to reliably determine the sequence of a typing gene, matching sequence reads for both strands of the gene must be obtained. This study assesses the ability of both the standard, and an alternative set of, Streptococcus pneumoniae MLST primers to completely sequence, in both directions, the required typing alleles. Results: The results demonstrated that for five (aroE, recP, spi, xpt, ddl) of the seven S. pneumoniae typing alleles, the standard primers were unable to obtain the complete forward and reverse sequences. This is due to the standard primers annealing too closely to the target regions, and current sequencing technology failing to sequence the bases that are too close to the primer. The alternative primer set described here, which includes a combination of primers proposed by the CDC and several designed as part of this study, addresses this limitation by annealing to highly conserved segments further from the target region. This primer set was subsequently employed to sequence type 105 S. pneumoniae isolates collected by the Canadian Immunization Monitoring Program ACTive (IMPACT) over a period of 18 years. Conclusions: The inability of several of the standard S. pneumoniae MLST primers to fully sequence the required region was consistently observed and is the result of a shift in sequencing technology occurring after the original primers were designed. The results presented here introduce clear documentation describing this phenomenon into the literature, and provide additional guidance, through the introduction of a widely validated set of alternative primers, to research groups seeking to undertake S. pneumoniae MLST based studies. © 2014 Adamiak et al.; licensee BioMed Central Ltd. Source

Peirano G.,535 Research Rd Nw | Peirano G.,University of Calgary | Ahmed-Bentley J.,Calgary DynaLife Diagnostic Laboratories Services | Woodford N.,Public Health England | And 2 more authors.
Emerging Infectious Diseases

An Escherichia coli isolate with New Delhi metallo-β-lactamase was isolated from a patient with pyelonephritis and prostatitis who returned to Canada after recent hospitalization in India. The patient was successfully treated with ertapenem and fosfomycin. This patient highlights the role of international travel in the spread of antimicrobial drug resistance and bla NDM-1. Source

Thommasen A.,University of Calgary | Clement F.,University of Calgary | Kinniburgh D.W.,University of Calgary | Lau C.K.,535 Research Rd Nw | And 9 more authors.
Clinical Biochemistry

Objectives: Mitigation of unnecessary and redundant laboratory testing is an important quality assurance priority for laboratories and represents an opportunity for cost savings in the health care system. Family physicians represent the largest utilizers of laboratory testing by a large margin. Engagement of family physicians is therefore key to any laboratory utilization management initiatives. Despite this, family physicians have been largely excluded from the planning and implementation of such initiatives. Our purposes were to (1) assess the importance of lab management issues to family physicians, and (2) attempt to define the types of initiatives most acceptable to family physicians. Design and methods: We invited all Alberta family practice residents and practicing physicians to participate in a self-administered online electronic survey. Survey questions addressed the perceived importance of lab misutilization, prevalence of various types of misutilization, acceptability of specific approaches to quality control, and responsibility of various parties to address this issue. Results: Of 162 respondents, 95% considered lab misutilization to be either important or very important. Many physicians placed the responsibility for addressing lab misutilization issues on multiple parties, including patients, but most commonly the ordering physician (97%). Acceptability for common strategies for quality improvement in lab misutilization showed a wide range (35%-98%). Conclusions: These responses could serve as a framework for laboratories to begin discussions on this important topic with primary care groups. © 2015 The Canadian Society of Clinical Chemists. Source

Interest in the use of biochar as soil amendment has grown recently. However, studies evaluating its potential use for reclamation of disturbed agricultural lands are lacking. We studied the effects of amending clay, loam, and sand subsoil substrates with wood biochar pyrolized at 800°C, oxidized lignite (humalite), or labile organic mix (sawdust, wheat straw, and alfalfa; LOM) on soil organic carbon (C), microbial biomass, dry aggregated size distribution and penetration resistance in greenhouse. We also considered the co-application of LOM and biochar or humalite to the subsoil substrates as treatments where C from either biochar or humalite represented a stable form of C. The amount and composition of the mix of organic amendments was determined for each subsoil so that organic C levels of reconstructed topsoil would be equivalent to that of the corresponding native topsoil in the long term. Field pea (Pisum sativum L.) and barley (Hordeum vulgare L.) were grown in rotation in four sequential greenhouse studies. Results from soil analysis at the end of study II and study IV showed that subsoils amended with biochar or humalite had higher organic C than those with LOM only, regardless of soil type. Labile organic mix added alone or together with biochar or humalite to subsoil increased microbial biomass and decreased geometric mean diameter of the dry soil aggregates. The effects of biochar or humalite-only amendment on these soil properties were not significant relative to the unamended subsoil substrate. Simultaneous application of biochar or humalite with LOM can potentially be used for topsoil reconstruction and reclamation of disturbed agricultural lands, and to maintain soil quality in the long term. However, long-term field studies are required to ascertain the longevity of the desirable properties reported in this study and to assess effects associated with aging of biochar or humalite in the soil. © 2015, Agricultural Institute of Canada. All rights reserved. Source

Baskin L.,535 Research Rd Nw | Baskin L.,University of Calgary | Abdullah A.,535 Research Rd Nw | Abdullah A.,University of Calgary | And 3 more authors.
American Journal of Clinical Pathology

Objectives: Approaches to determining optimal locations for patient service centers (phlebotomy clinics) have not been addressed in the published literature. Using the city of Calgary, Alberta, Canada, as a test case, our objective is to present a novel method for determining underserviced geographic areas within a city to guide the choice of potential new patient service center locations. Methods: Data on travel distances for 198,883 phlebotomy visits as well as population data from the 2011 Canada Census were used for this study. Using geospatial mapping techniques, we produced maps of the city showing actual relative travel distances for patients as well as the geographic distribution of population density of patients undergoing phlebotomies. Results: There was a striking pattern of increased travel distances in certain parts of the city. These also corresponded to geographic areas with greater density of patients seeking phlebotomies. Conclusions: This analysis provided clear, objective evidence of communities that are currently relatively underserved by patient service centers. This approach could be used by other laboratories to plan the location of new patient service centers. © American Society for Clinical Pathology. Source

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