Outbreak of Escherichia coli O157:H7 gastroenteritis associated with consumption of beef donairs, Edmonton, Alberta, May-June 2006.
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Adolescent↗
Biomedical subjects
L Chui
Publications and source records attributed to L Chui.
The use of randomization tests to assess the degree of similarity in PFGE patterns of E. coli O157 isolates from known outbreaks and statistical space-time clusters.
Using isolates from reported cases of Escherichia coli O157 from Alberta, Canada in 2002, we applied randomization tests to determine if cases associated with an outbreak or statistical space-time cluster had more similar pulsed-field gel electrophoresis patterns, based on Dice coefficients, than expected by chance alone. Within each outbreak and space-time cluster, we assessed the mean, median, 25th percentile, 75th percentile, standard deviation, coefficient of variation, and interquartile range of the Dice coefficients of each pairwise comparison among the isolates. To assess the statistical significance of measures of location (e.g. mean) and variation (e.g. standard deviation) we created randomization distributions using all isolates or only isolates from sporadic cases. We determined that randomization tests are an appropriate tool for evaluating the similarity among isolates from cases that have been linked epidemiologically or statistically. We found little difference between using all cases or only sporadic cases when creating our randomization distributions.
Disease Outbreaks↗
The use of outbreak information in the interpretation of clustering of reported cases of Escherichia coli O157 in space and time in Alberta, Canada, 2000-2002.
We obtained a list of all reported cases of Escherichia coli O157 in Alberta during the 2000-2002 period, and using scan statistics we identified yearly temporal and spatial clusters of reported cases of E. coli O157 during the summer and in southern Alberta. However, the location of the spatial cluster in the south was variable among years. The impact of using both outbreak and sporadic data or only sporadic data on the identification of spatial and temporal clusters was small when analysing individual years, but the difference between spatial clusters was pronounced when scanning the entire study period. We also identified space-time clusters that incorporated known outbreaks, and clusters that were suggestive of undetected outbreaks that we attempted to validate with molecular data. Our results suggest that scan statistics, based on a space-time permutation model, may have a role in outbreak investigation and surveillance programmes by identifying previously undetected outbreaks.
Alberta↗
Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens.
The emergence of a novel coronavirus (CoV) as the cause of severe acute respiratory syndrome (SARS) catalyzed the development of rapid diagnostic tests. Stool samples have been shown to be appropriate for diagnostic testing for SARS CoV, although it has been recognized to be a heterogeneous and difficult sample that contains amplification inhibitors. Limited information on the efficiency of extraction methods for the purification and concentration of SARS CoV RNA from stool samples is available. Our study objectives were to determine the optimal extraction method for SARS CoV RNA detection and to examine the effect of increased specimen volume for the detection of SARS CoV RNA in stool specimens. We conducted a multicenter evaluation of four automated and four manual extraction methods using dilutions of viral lysate in replicate mock stool samples, followed by quantitation of SARS CoV RNA using real-time reverse transcriptase PCR. The sensitivities of the manual methods ranged from 50% to 100%, with the Cortex Biochem Magazorb method, a magnetic bead isolation method, allowing detection of all 12 positive samples. The sensitivities of the automated methods ranged from 75% to 100%. The bioMérieux NucliSens automated extractor and miniMag extraction methods each had a sensitivity of 100%. Examination of the copy numbers detected and the generation of 10-fold dilutions of the extracted material indicated that a number of extraction methods retained inhibitory substances that prevented optimal amplification. Increasing the volume of sample input did improve detection. This information could be useful for the extraction of other RNA viruses from stool samples and demonstrates the need to evaluate extraction methods for different specimen types.
Feces↗
Transmission characteristics of tuberculosis in the foreign-born and the Canadian-born populations of Alberta, Canada.
SETTING: All notified cases of tuberculosis in the province of Alberta, Canada, 1994-1998. OBJECTIVE: To compare the transmission characteristics of tuberculosis among foreign-born and Canadian-born cases. DESIGN: Retrospective analysis using DNA fingerprinting (IS6110 restriction fragment length polymorphism and spoligotyping) and patient information from the Alberta Tuberculosis Registry. Transmission indexes were determined by calculating the average number of culture-positive pulmonary cases generated by a single source case. RESULTS: Of the 750 cases of active tuberculosis, 437 (58.3%) were in the foreign-born. DNA fingerprinting of Mycobacterium tuberculosis isolates from all 573 culture-positive cases over the 5 years from 1994 to 1998 showed that there was significantly less clustering among foreign-born isolates (9.8%) compared to Canadian-born non-Aboriginal (28.8%) and Aboriginal (44.7%) isolates. The transmission index was significantly higher for males, lower for those > or =65 years of age, and higher for Aboriginals. CONCLUSION: Although cases of tuberculosis in the foreign-born constitute the majority in Alberta, there is little transmission to other foreign-born or to Canadian-born individuals. Transmission of tuberculosis among the Aboriginal population remains a significant problem in Alberta.
Adult↗
Outbreak of Salmonella paratyphi B var java due to contaminated alfalfa sprouts in Alberta, British Columbia and Saskatchewan.
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British Columbia↗
Postsanatorium pattern of antituberculous drug resistance in the Canadian-born population of western Canada: effect of outpatient care and immigration.
Concurrent with the shift in tuberculosis case management from sanatorium to outpatient setting was a shift in the continent of origin (Europe to Asia) of most new immigrants to CANADA: To assess the impact of these two events on antituberculous drug resistance in the Canadian-born population, the authors reviewed the results of six drug resistance surveys conducted in the two westernmost provinces of Canada between 1963 and 1994. Survey data were complemented by new molecular diagnostic and contact tracing data collected over 5 years (1994--1998) in one of the three large urban centers of the region. Over the time spanned by the surveys, there was no increase in the proportion of all Canadian-born tuberculosis cases who relapsed or the proportion of all Canadian-born relapsed cases who were drug resistant (approximately 12--13%). In addition, the prevalence of primary drug resistance among Canadian-born cases did not increase; rates consistently averaged between 2% and 5% despite a doubling of primary resistance rates among foreign-born cases. Molecular diagnostic and contact tracing data strongly supported the survey findings. The authors concluded that outpatient care and immigration have thus far had no measurable impact on the pattern of antituberculous drug resistance in the Canadian-born population of western CANADA:
Adolescent↗
Development of a Canadian standardized protocol for subtyping methicillin-resistant Staphylococcus aureus using pulsed-field gel electrophoresis.
A panel of 24 methicillin-resistant Staphylococcus aureus strains was distributed to 15 laboratories in Canada to evaluate their in-house pulsed-field gel electrophoresis (PFGE) protocols and interpretation criteria. Attempts to compare fingerprint images using computer-aided analysis were not successful due to variability in individual laboratory PFGE protocols. In addition, individual site interpretation of the fingerprint patterns was inadequate, as 7 of 13 sites (54%) made at least one error in interpreting the fingerprints from the panel. A 2-day standardized PFGE protocol (culture to gel image) was developed and distributed to all of the sites. Each site was requested to use the standardized protocol on five strains from the original panel. Thirteen sites submitted gel images for comparisons. The protocol demonstrated excellent reproducibility and allowed interlaboratory comparisons with Molecular Analyst DST software (Bio-Rad) and 1.5% band tolerance.
Bacterial Typing Techniques↗
Comparison and application of a novel genotyping method, semiautomated primer-specific and mispair extension analysis, and four other genotyping assays for detection of hepatitis C virus mixed-genotype infections.
To date the true prevalence of hepatitis C virus (HCV) mixed-genotype infections has not been established mainly because currently available methods are not suitable for the detection of mixed genotypes in a viral population. A novel semiautomated genotyping method, primer-specific and mispair extension analysis (S-PSMEA), which is more reliable than other genotyping assays was developed for detection of HCV mixed-genotype infections. A genotype present at levels as low as 0.8% in a defined mix of HCV genotypes was detected, showing a 20-fold increase in sensitivity over that of direct DNA sequencing. A total of 434 HCV isolates were genotyped and analyzed for a comparative study of the accuracy between S-PSMEA and four current genotyping methods. The results showed that viruses in approximately 40% of the samples from this group determined to be infected with mixed genotypes by S-PSMEA were undetected by direct DNA sequencing due to its low sensitivity. Type-specific PCR, line probe assay, and restriction fragment length polymorphism analysis performed poorly, being able to identify only 38.5, 16.1, and 15.4% of mixed-genotype infections, respectively, that were detected by direct DNA sequencing. The prevalence of mixed-genotype infections detected by S-PSMEA was 7.9% (12 of 152 donors) among HCV-infected blood donors, 14.3% (15 of 105) among patients with chronic hepatitis C, and 17.1% (6 of 36) among thalassemia patients who had received multiple transfusions. The data lead us to conclude that HCV mixed-genotype infections are more common than previously estimated and that S-PSMEA may be the method of choice when detection of genotypes present at low levels in mixed-genotype infections is required due to its higher level of sensitivity.
Base Pair Mismatch↗
Cross-Canada spread of methicillin-resistant Staphylococcus aureus via transplant organs.
We report our investigation of the transmission of methicillin-resistant Staphylococcus aureus (MRSA) through transplantation. The kidneys, liver, and corneas were harvested from a child who died in Nova Scotia. Several days postmortem it was learned that culture of a premortem endotracheal tube aspirate from the donor yielded MRSA. Both kidneys were transplanted into a child in Nova Scotia and the liver into a child in Alberta. Both recipients subsequently became blood culture-positive for MRSA. One corneal ring from the donor was MRSA-positive. All four MRSA isolates were mecA-positive by polymerase chain reaction (PCR). The relatedness of the MRSA isolates was examined by restriction fragment length polymorphism (RFLP) analysis, a 16S-23S ribosomal PCR typing method, and comparison of antibiograms. Results were identical for all four MRSA isolates. These findings indicate that MRSA from the donor was transferred to recipients during implantation of harvested organs in Alberta and Nova Scotia, a cross-Canada spread.
Adolescent↗
Immune mediated 'HAART' attack during treatment for tuberculosis. Highly active antiretroviral therapy.
Highly active antiretroviral therapy (HAART) suppresses viral replication and improves immune function. However the inflammatory component of immune restoration can have clinically deleterious effects on previously asymptomatic infections. We report the development of acute respiratory failure in a patient after the institution of HAART, following 2 months of appropriate therapy for pulmonary tuberculosis. Necrotizing granulomas with acid-fast bacilli were found on lung biopsy, but cultures were negative for Mycobacterium tuberculosis and no other pathogens were isolated. Polymerase chain reaction of lung biopsy tissue for all mycobacterial species was positive only for M. tuberculosis. Rapid clinical improvement followed corticosteroid therapy. After initiating HAART, clinicians should be aware of the possibility of an inflammatory response to a previously quiescent tuberculous infection, even while on antituberculosis therapy.
AIDS-Related Opportunistic Infections↗
A standardized protocol for the rapid preparation of bacterial DNA for pulsed-field gel electrophoresis.
A rapid method for the preparation of bacterial DNA for pulsed-field gel electrophoresis was developed for Gram-positive and Gram-negative bacteria. This method was accomplished by reducing the time for the cell lysis reaction, restriction endonuclease digestion, and electrophoresis to 1, 1.5, and 18 h, respectively. The whole procedure from the initial bacterial culture plate to the final analysis of restriction fragments can be completed within 24 h. This rapid method was successfully achieved for Staphylococcus aureus, Enterococcus faecalis, Neisseria gonorrhoeae, Salmonella typhimurium, Serratia marcescens, and Stenotrophomonas maltophilia.
Bacteriological Techniques↗
An algorithm to detect Chlamydia trachomatis by polymerase chain reaction on specimens extracted for enzyme immunoassay.
Amplification assays for detecting Chlamydia trachomatis have been shown to be more sensitive than enzyme immunoassay (EIA) by many investigators. In this study, we have developed an algorithm for performing PCR (COBAS AMPLICOR) on selected specimens extracted for EIA (ACCESS) with sample-to-cutoff (s/co) values between 0.25 and 0.99. Furthermore, we have shown that these specimens can be utilized for PCR without encountering any inhibition problems. In our investigation, 230 out of 6,558 urethral and cervical swabs submitted for C. trachomatis screening by EIA over a period of 9 months, had s/co values ranging between of 0.25 and 0.99. Ninety (39.1%) of these specimens tested positive by PCR. These specimens were stable and gave reproducible PCR results before and after storage for a period of 9 months. This testing algorithm offers an effective way of detecting C. trachomatis with selective use of PCR while increasing the sensitivity of the EIA screening system.
Algorithms↗
Central venous catheters as a source of hemodialysis-related bacteremia.
OBJECTIVE: To describe investigations into an increase in hemodialysis-related bacteremia that occurred in our hospital in the first 6 months of 1996. SETTING: Hemodialysis unit in a tertiary-care medical center. METHODS: Prospective surveillance for hemodialysis bacteremia has been performed for several years. Cases that occurred in 1995 were compared to cases in the first 6 months of 1996. Unit data on dialysis runs and method of dialysis access were used to calculate rates. Nested polymerase chain reaction (PCR) was used to type 18 Staphylococcus aureus isolates from 1996. A case-control study comparing 80 randomly selected hemodialysis patients from 1995 and 1996 was performed to examine infection risk factors. RESULTS: The hemodialysis bacteremia rate was 1.2 per 1,000 runs in 1995 and 2.8 per 1,000 in the first 6 months of 1996 (P=.0009). The 25 cases in 1995 and 32 in the first half of 1996 were similar in age, gender, means of vascular access, and microbial etiology. Central venous catheter (CVC) access accounted for >90% of cases in both time periods. S aureus was the most common microbial etiology (53% of the 1996 cases). PCR typing of S aureus isolates from 1996 demonstrated five different strains, the most common having six isolates. The use of CVCs as a means of vascular access abruptly increased in the unit in January 1996, from <30% of dialysis runs in 1995 to >40% in 1996 (P<.001), associated with structural changes in healthcare delivery in the region resulting in delays in performing surgical procedures, such as creation of vascular grafts and fistulae. CONCLUSION: A marked increase in hemodialysis bacteremia occurred in 1996, associated with increased reliance on CVCs for vascular access in hemodialysis patients during a period of healthcare restructuring.
Adult↗
Epitope analysis of a sperm acrosomal antigen defined by HSA-5 monoclonal antibody.
Among the monoclonal antibodies recommended by the WHO Sperm Antigen Workshop for immunocontraceptive vaccine development, HSA-5 showed a high degree of sperm specificity and significantly inhibited in vitro fertilization in both humans and mice. Using a Western blot assay, HSA-5 was found to recognize a sperm antigen designated as HSAg-5 (human) or MSAg-5 (mouse) which ranged in molecular weight from 18 to 100 kDa. This monoclonal antibody was used as the probe for the immunoscreening of mouse testis cDNA libraries constructed in the lambda gt-11 expression vector. One of the positive cDNA clones was shown to have a cDNA insert of approximately 1 kb and to encode a recombinant fusion protein containing 77 amino acid residues in the C-terminal region of MSAg-5. This 1 kb cDNA insert was engineered in a pGEX vector to express a recombinant glutathione S-transferase fusion protein (GST-5). Using an enzyme-linked immunosorbent assay (ELISA) and Western blot analysis, both anti-GST-5 sera and the monoclonal antibody were shown to react with GST-5. The Northern blot of a mouse testis RNA preparation revealed that the isolated cDNA probe hybridized with a 4.0 kb mRNA. Several oligopeptides were synthesized based on the predicted C-terminal hydrophilic regions of the recombinant fusion protein. Using ELISA and a dot blot assay, peptide regions containing the immunogenic epitopes recognized by HSA-5 monoclonal antibody were identified.
Amino Acid Sequence↗
Sequence analysis of two deletion mutants in the hisC gene of Salmonella typhimurium.
Limited sequencing of the terminal region of the hisC gene in two deletion mutants involving the hisC gene of Salmonella typhimurium was carried out after polymerase chain reaction amplification of the appropriate region, using oligonucleotide primers selected from the published sequence of the histidine operon from this organism. his2648 was shown to have a 34 base pair deletion in the terminal region of the hisC gene between the P2 promoter and the Shine-Delgarno sequence of the hisB gene. hisHB22 was shown to have a 1.4 kilobase deletion extending from the TGA termination codon of the hisC gene to the middle of the hisH gene. The sequence data were consistent with previous genetic and phenotypic characterization of these strains.
Bacterial Proteins↗
Development of the polymerase chain reaction for diagnosis of chancroid.
The published nucleotide sequences of the 16S rRNA gene of Haemophilus ducreyi were used to develop primer sets and probes for the diagnosis of chancroid by polymerase chain reaction (PCR) DNA amplification. One set of broad specificity primers yielded a 303-bp PCR product from all bacteria tested. Two 16-base probes internal to this sequence were species specific for H. ducreyi when tested with 12 species of the families Pasteurellaceae and Enterobacteriaceae. The two probes in combination with the broad specificity primers were 100% sensitive with 51 strains of H. ducreyi isolated from six continents over a 15-year period. The direct detection of H. ducreyi from 100 clinical specimens by PCR showed a sensitivity of 83 to 98% and a specificity of 51 to 67%, depending on the number of amplification cycles.
Base Sequence↗
The use of MRI in the identification of post-traumatic laryngeal deformities.
Suspected post-traumatic deformity of the laryngeal cartilages can be diagnosed by using current magnetic resonance imaging (MRI) scanning techniques. This is of particular aid to the clinician who is evaluating a laryngeal mass with no history of injury to the neck. Computed tomography (CT) and magnetic resonance imaging are both effective in this situation, but MRI appreciates better soft tissue contrast, and can offer coronal and sagittal views.
Aged↗