Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Trends in Population Dynamics of Escherichia coli Sequence Type 131, Calgary, Alberta, Canada, 2006-2016¹.

ABSTRACT: Global expansion of antimicrobial drug-resistant Escherichia coli sequence type (ST) 131 is unrivaled among human bacteria. Understanding trends among ST131 clades will help with designing prevention strategies. We screened E. coli from blood samples (n = 1,784) obtained in Calgary, Alberta, Canada, during 2006, 2012, and 2016 by PCR for ST131 and positive samples (n = 344) underwent whole-genome sequencing. The incidence rate per 100,000 residents increased from 4.91 during 2006 to 12.35 during 2012 and 10.12 during 2016. ST131 belonged to clades A (10%), B (9%), and C (81%). Clades C1-nonM27 and B were common during 2006, and C2 containing bla_CTX-M-15, C1-M27 containing bla_CTX-M-27, and A were responsible for the increase of ST131 during 2012 and 2016. C2 was the most antimicrobial drug-resistant subclade and increased exponentially over time. Eradicating ST131, more specifically the C2 subclade, will lead to considerable public health benefits for persons in Calgary.

SUBMITTER: Peirano G

PROVIDER: S-EPMC7706940 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Epidemiology of Shiga Toxin-Producing Escherichia coli O157 in the Province of Alberta, Canada, 2009-2016.

Project description:Shiga toxin-producing Escherichia coli (STEC) infections are the product of the interaction between bacteria, phages, animals, humans, and the environment. In the late 1980s, Alberta had one of the highest incidences of STEC infections in North America. Herein, we revisit and contextualize the epidemiology of STEC O157 human infections in Alberta for the period 2009-2016. STEC O157 infections were concentrated in large urban centers, but also in rural areas with high cattle density. Hospitalization was often required when the Shiga toxin genotype stx2a stx2c was involved, however, only those aged 60 years or older and infection during spring months (April to June) independently predicted that need. Since the late 1980s, the rate of STEC O157-associated hemolytic uremic syndrome (HUS) in Alberta has remained unchanged at 5.1%, despite a marked drop in the overall incidence of the infection. While Shiga toxin genotypes stx1a stx2c and stx2a stx2c seemed associated with HUS, only those aged under 10 years and infection during spring months were independently predictive of that complication. The complexity of the current epidemiology of STEC O157 in Alberta highlights the need for a One Health approach for further progress to be made in mitigating STEC morbidity.

| S-EPMC6832344 | biostudies-literature

Trauma Association of Canada Annual Scientific Meeting, Westin Calgary Calgary, Alberta, Apr. 10–11, 2015

Project description: Not available

| S-EPMC8186475 | biostudies-literature

The incidence of acute myeloid leukemia in Calgary, Alberta, Canada: a retrospective cohort study.

Project description:The incidence rate of acute myeloid leukemia (AML) was determined in the Calgary Metropolitan Area, a major Canadian city.Data from all patients diagnosed with AML between January 1, 2011 and December 31, 2015 were retrieved from a single, centralized cancer cytogenetics laboratory for bone marrow samples, the sole diagnostic facility of its kind in Southern Alberta.The calculated incidence rate was 2.79 cases per 100,000 person-years with a median age of 60, slightly lower than previously published data. The age-standardized incidence rate for Canada was 3.46 cases per 100,000 person-years. The higher value is reflective of Calgary's younger population compared to the rest of Canada. Higher male incidence and greatest incidence occurring at approximately the age of 85 is similar to data from other developed countries. The lower incidence rates and median age of diagnosis, in comparison with that of other high-income nations, may be due to differences in the proportion of aging citizens in the population.This is the first published incidence rate of acute myeloid leukemia (AML) in Canada across all age groups.

| S-EPMC5543578 | biostudies-other

Test volume data for 51 most commonly ordered laboratory tests in Calgary, Alberta, Canada.

Project description:Data presented in this article include the top 51 ordered laboratory tests in Calgary and surrounding area, Alberta, from January to December 2017. This data set was collected from Calgary Laboratory Service's Laboratory Information System, and included top 51 tests ordered from community (n = 11, 224, 330), inpatient (n = 2,340,594) and emergency (n = 1,670,062) settings. Test order mnemonic that were not true laboratory tests (eg: "extra PST tube", "extra tube", etc.) were excluded in the analysis. The top test ordered in all 3 test encounters was the complete blood count test (community encounter, n = 921, 873; inpatient setting, n = 357, 375; and emergency setting, n = 276, 954). This data article was submitted as a companion paper to the related research article, "Estimated costs of 51 commonly ordered laboratory tests in Canada" [1].

| S-EPMC6660485 | biostudies-literature

Trends in engagement in the cascade of care for opioid use disorder, Vancouver, Canada, 2006-2016.

Project description:BACKGROUND:A cascade of care framework has been proposed to identify and address implementation gaps in addiction medicine. Using this framework, we characterized temporal trends in engagement in care for opioid use disorder (OUD) in Vancouver, Canada. METHODS:Using data from two cohorts of people who use drugs, we assessed the yearly proportion of daily opioid users achieving four sequential stages of the OUD cascade of care [linkage to addiction care; linkage to opioid agonist treatment (OAT); retention in OAT; and stability] between 2006 and 2016. We evaluated temporal trends of cascade indicators, adjusting for socio-demographic characteristics, HIV/HCV status, substance use patterns, and social-structural exposures. RESULTS:We included 1615 daily opioid users. Between 2006 and 2016, we observed improvements in linkage to care (from 73.2% to 78.9%, p?=?<0.001), linkage to (from 69.2% to 70.6%, p?=?0.011) and retention in OAT (from 29.1% to 35.5%, p?=?<0.001), and stability (from 10.4% to 17.1%, p?=?<0.001). In adjusted analyses, later calendar year of observation was associated with increased odds of linkage to care (Adjusted Odds Ratio [AOR]?=?1.02, 95% Confidence Interval [CI]: 1.01-1.04), retention in OAT (AOR 1.02, 95% CI: 1.01-1.04) and stability (AOR?=?1.03, 95% CI: 1.01-1.05), but not with linkage to OAT (AOR 1.00, 95% CI: 0.98-1.01). CONCLUSIONS:Temporal improvements in OUD cascade of care indicators were observed. However, only a third of participants were retained in OAT in 2016. These findings suggest the need for novel approaches to improve engagement in care for OUD to address the escalating opioid-related overdose crisis.

| S-EPMC6062451 | biostudies-literature

Dataset of clinical laboratory tests according to ordering variance among family physicians in Calgary, Alberta, Canada.

Project description:This data incorporates 2016 testing volumes ordered by family physicians and performed at Calgary Laboratory Services (CLS), the sole supplier of clinical laboratory services for the catchment area of the City of Calgary, Alberta, Canada. For each test, the mean number of tests ordered per patient was calculated over ordering Calgary physicians, along with arithmetic coefficients of variation (CV's). The latter parameter is reflective of variance in ordering practice among family physicians practicing in Calgary and is proposed as a benchmark measure for laboratory utilization in our accompanying research article [1]. The data table encompasses 358 tests ordered by at least 3 family physicians at a minimum total frequency of 100 within the 2016 study period and is presented in ascending order of rank in CV.

| S-EPMC6717211 | biostudies-literature

Community data of adults fasting for lipid and diabetes tests in Calgary, Alberta from 2010 to 2016.

Project description:Data presented in this data article include the proportion and counts of community-based adult men and women who fasted for various lipid and diabetes screening-related tests from January 2010 to June 2016 in Calgary, Alberta, Canada. This data set was collected from Calgary Laboratory Service׳s Laboratory Information System, and included 3,003,667 testing encounters (1,447,720 testing encounters for men and 1,555,947 testing encounters for women) over the age of 18 years, who fasted for a lipid profile, lipid+random blood glucose (RBG), lipid+hemoglobin A1c (HbA1c), lipid+RBG+HbA1c, lipid+fasting blood glucose (FBG), lipid+FBG+RBG, lipid+FBG+HbA1c, or lipid+FBG+RBG+HbA1c. Data are related to "Proportion of adults fasting for lipid testing relative to guideline changes in Alberta" (Ma et al., 2017).

| S-EPMC6307346 | biostudies-literature

Identifying and critically examining government legislation relevant to children's dental caries in Calgary, Alberta, Canada: a health inequities lens.

Project description:ObjectivesChildren's dental caries is an important and urgent public health concern that is largely preventable. Using a social equity framework, our objectives were to identify and critically examine government legislation relevant to the issue of children's dental health in Calgary, Alberta, Canada.MethodsWe conducted a systematic, gray literature search of federal, provincial (Alberta), and municipal (Calgary) statutes and bylaws related to children's dental caries, through the relevant law databases. Eligibility criteria were applied for document screening and selection. Data extraction and synthesis pertained to objectives of the legislation (policy task), relevant agent or actor (level of government), and upstream or downstream focus, in terms of potential impact on social inequities in health.ResultsLegislation (n = 114) was retrieved and grouped into eight policy tasks. Most legislation fit under the policy tasks: protection of public safety and health promotion (n = 40) and benefits and compensation (n = 27). Federal and provincial governments have greater involvement in children's dental caries than municipal (Calgary) government. The majority of legislation was classified as upstream in orientation (e.g., improving living and working conditions; macro-level policies).ConclusionsAnalysis of legislation relevant to children's dental caries reveals policies that are more often upstream in nature, and unsurprisingly are multijurisdictional. Despite this, there remains a high prevalence and inequitable distribution of children's dental caries in Canada. This suggests that the nature of upstream involvement and fragmented government involvement is ineffective in tackling this pervasive and urgent public health issue. Implications for children's dental health are discussed.

| S-EPMC6850351 | biostudies-literature

Genome Sequences of 104 Escherichia coli O157:H7 Isolates from Pigs, Cattle, and Pork Production Environments in Alberta, Canada.

Project description:Genome sequences of Escherichia coli O157:H7 originating from pigs are limited in the public databases. We sequenced 104 E. coli O157:H7 isolates from pig and cattle feces and pork production environments in Alberta, Canada. The information will aid studies investigating sources of E. coli O157:H7 contaminating pork and the associated environments.

| S-EPMC7844076 | biostudies-literature

Rapid Identification of Different Escherichia coli Sequence Type 131 Clades.

Project description:Escherichia coli sequence type 131 (ST131) is a pandemic clonal lineage that is responsible for the global increase in fluoroquinolone resistance and extended-spectrum-β-lactamase (ESBL) producers. The members of ST131 clade C, especially subclades C2 and C1-M27, are associated with ESBLs. We developed a multiplex conventional PCR assay with the ability to detect all ST131 clades (A, B, and C), as well as C subclades (C1-M27, C1-nM27 [C1-non-M27], and C2). To validate the assay, we used 80 ST131 global isolates that had been fully sequenced. We then used the assay to define the prevalence of each clade in two Japanese collections consisting of 460 ESBL-producing E. coli ST131 (2001-12) and 329 E. coli isolates from extraintestinal sites (ExPEC) (2014). The assay correctly identified the different clades in all 80 global isolates: clades A (n = 12), B (n = 12), and C, including subclades C1-M27 (n = 16), C1-nM27 (n = 20), C2 (n = 17), and other C (n = 3). The assay also detected all 565 ST131 isolates in both collections without any false positives. Isolates from clades A (n = 54), B (n = 23), and C (n = 483) corresponded to the O serotypes and the fimH types of O16-H41, O25b-H22, and O25b-H30, respectively. Of the 483 clade C isolates, C1-M27 was the most common subclade (36%), followed by C1-nM27 (32%) and C2 (15%). The C1-M27 subclade with blaCTX-M-27 became especially prominent after 2009. Our novel multiplex PCR assay revealed the predominance of the C1-M27 subclade in recent Japanese ESBL-producing E. coli isolates and is a promising tool for epidemiological studies of ST131.

| S-EPMC5527616 | biostudies-literature