Publications by authors named "Linda Hoang"

129 Publications

Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage.

Antibiotics (Basel) 2022 Jul 15;11(7). Epub 2022 Jul 15.

Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada.

Antibiotic resistance is a global health crisis increasing in prevalence every day. To combat this crisis, alternative antimicrobial therapeutics are urgently needed. Antimicrobial peptides (AMPs), a family of short defense proteins, are produced naturally by all organisms and hold great potential as effective alternatives to small molecule antibiotics. Here, we present rAMPage, a scalable bioinformatics discovery platform for identifying AMP sequences from RNA sequencing (RNA-seq) datasets. In our study, we demonstrate the utility and scalability of rAMPage, running it on 84 publicly available RNA-seq datasets from 75 amphibian and insect species-species known to have rich AMP repertoires. Across these datasets, we identified 1137 putative AMPs, 1024 of which were deemed novel by a homology search in cataloged AMPs in public databases. We selected 21 peptide sequences from this set for antimicrobial susceptibility testing against and and observed that seven of them have high antimicrobial activity. Our study illustrates how in silico methods such as rAMPage can enable the fast and efficient discovery of novel antimicrobial peptides as an effective first step in the strenuous process of antimicrobial drug development.
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http://dx.doi.org/10.3390/antibiotics11070952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9312091PMC
July 2022

Estimating population-based incidence of community-acquired pneumonia and acute otitis media in children and adults in Ontario and British Columbia using health administrative data, 2005-2018: a Canadian Immunisation Research Network (CIRN) study.

BMJ Open Respir Res 2022 06;9(1)

Centre for Vaccine Preventable Diseases, University of Toronto, Toronto, Ontario, Canada

Background: There is a paucity of data on the burden of the full spectrum of community-acquired pneumonia (CAP) and acute otitis media (AOM) from outpatient and inpatient settings across the age spectrum.

Methods: We conducted a population-based retrospective study in Ontario and British Columbia (BC), Canada, to estimate the incidence rate of CAP and AOM in children and adults over a 14-year period using health administrative databases. CAP and AOM cases were identified from outpatient physician consultation and hospitalisation data in both provinces, and from emergency department visit data in Ontario.

Results: During 2005-2018, Ontario had 3 607 124 CAP, 172 290 bacterial CAP, 7814 pneumococcal pneumonia, and 8 026 971 AOM cases. The incidence rate of CAP declined from 3077/100 000 in 2005 to 2604/100 000 in 2010 before increasing to 2843/100 000 in 2018; bacterial CAP incidence rate also declined from 178/100 000 in 2005 to 112/100 000 in 2010 before increasing to 149/100 000 in 2018. The incidence rate of AOM decreased from 4192/100 000 in 2005 to 3178/100 000 in 2018. BC had 970 455 CAP, 317 913 bacterial CAP, 35 287 pneumococcal pneumonia and 2 022 871 AOM cases. The incidence rate of CAP in BC decreased from 2214/100 000 in 2005 to 1964/100 000 in 2010 before increasing to 2176/100 000 in 2018; bacterial CAP incidence rate increased from 442/100 000 in 2005 to 981/100 000 in 2018. The incidence rate of AOM decreased from 3684/100 000 in 2005 to 2398/100 000 in 2018. The incidence rate of bacterial CAP increased with age in older adults (≥65 years) with the highest burden in the oldest cohort aged ≥85 years both before and after 13-valent pneumococcal conjugate vaccine (PCV13) programme in both provinces. Hospitalised pneumococcal pneumonia decreased slightly but non-hospitalised pneumococcal pneumonia increased in BC during PCV13 period. No consistent direct benefit of PCV13 on CAP was observed in the paediatric population.

Conclusions: There is a substantial burden of CAP and AOM in Ontario and BC. Indirect benefits from childhood PCV vaccination and polysaccharide vaccination of older adults have not substantially decreased the burden of pneumococcal pneumonia in older adults.
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http://dx.doi.org/10.1136/bmjresp-2022-001218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9240885PMC
June 2022

One Health Genomic Analysis of Extended-Spectrum β-Lactamase‒Producing Salmonella enterica, Canada, 2012‒2016.

Emerg Infect Dis 2022 07;28(7):1410-1420

Extended-spectrum β-lactamases (ESBLs) confer resistance to extended-spectrum cephalosporins, a major class of clinical antimicrobial drugs. We used genomic analysis to investigate whether domestic food animals, retail meat, and pets were reservoirs of ESBL-producing Salmonella for human infection in Canada. Of 30,303 Salmonella isolates tested during 2012-2016, we detected 95 ESBL producers. ESBL serotypes and alleles were mostly different between humans (n = 54) and animals/meat (n = 41). Two exceptions were bla and bla IncI1 plasmids which were found in both sources. A subclade of S. enterica serovar Heidelberg isolates carrying the same IncI1-bla plasmid differed by only 1-7 single nucleotide variants. The most common ESBL producer in humans was Salmonella Infantis carrying bla, which has since emerged in poultry in other countries. There were few instances of similar isolates and plasmids, suggesting that domestic animals and retail meat might have been minor reservoirs of ESBL-producing Salmonella for human infection.
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http://dx.doi.org/10.3201/eid2807.211528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9239887PMC
July 2022

Limitation of as a Target for Neisseria meningitidis Identification and Potential Alternative Targets.

J Clin Microbiol 2022 06 23;60(6):e0015222. Epub 2022 May 23.

Division of Medical Microbiology, BC Children's Hospital and BC Women's Hospital & Health Centre, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1128/jcm.00152-22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9199397PMC
June 2022

Healthcare Costs for Pneumococcal Disease in the Era of Infant Immunization With 13-Valent Pneumococcal Conjugate Vaccine: A Population-Based Study.

Value Health 2022 Apr 21. Epub 2022 Apr 21.

Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada; School of Population and Public Health, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada. Electronic address:

Objectives: Invasive pneumococcal disease (IPD) and a variety of clinical syndromes caused by pneumococci, such as acute otitis media (AOM), acute sinusitis (AS), and community-acquired pneumonia (CAP), cause a substantial burden on healthcare systems. Few studies have explored the short-term financial burden of pneumococcal disease after the 13-valent pneumococcal conjugate vaccine (PCV13) introduction in the infant immunization programs. This population-based study evaluated changes in costs associated with healthcare utilization for pneumococcal disease after the PCV13 introduction in the infant immunization program in British Columbia, Canada.

Methods: Individuals with pneumococcal disease were identified using provincial administrative data for the 2000 to 2018 period. Total direct healthcare costs were determined using case-mix methodology for hospitalization and fee-for-service codes for outpatient visits and medications dispensed. Costs were adjusted to 2018 Canadian dollars. Changes in the annual healthcare costs were evaluated across vaccine eras (pre-PCV13, 2000-2010; PCV13, 2011-2018) using generalized linear models, adjusting for the 7-valent pneumococcal conjugate vaccine program (2004-2010).

Results: During the 19-year study period, pneumococcal disease resulted in 6.3 million cases among 85 million total patient-years, resulting in total healthcare costs of $7.9 billion. More than 6.2 million cases were treated in outpatient setting, costing $0.65 billion (8% of total costs associated with pneumococcal disease treatment), whereas 370 000 hospitalized cases were 3% of all cases, which accrued $7.25 billion (92% of total costs) in costs. Healthcare costs for all studied infections nearly doubled over the study period from $248 million in 2000 to $476 million in 2018 (P = .003). In contrast, there were large declines in total annual costs in the PCV13 era for IPD (adjusted relative rate (aRR) 0.73; 95% confidence interval [CI] 0.56-0.95; P = .032), AOM (aRR 0.70; 95% CI 0.59-0.83; P = .001), and AS (aRR 0.68; 95% CI 0.54-0.85; P = .004) compared with the pre-PCV13 era. Total costs increased marginally in the PCV13 era for all-cause CAP (aRR 1.04; 95% CI 0.94-1.15; P = .484).

Conclusions: This study confirms a temporal association in declining economic burden for IPD, AOM, and AS after the PCV13 introduction. Nevertheless, the total economic burden continues to be high in the PCV13 era, mainly driven by increasing CAP costs.
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http://dx.doi.org/10.1016/j.jval.2022.03.017DOI Listing
April 2022

Two-dose SARS-CoV-2 vaccine effectiveness with mixed schedules and extended dosing intervals: test-negative design studies from British Columbia and Quebec, Canada.

Clin Infect Dis 2022 Apr 19. Epub 2022 Apr 19.

BC Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada.

Background: The Canadian COVID-19 immunization strategy deferred second doses and allowed mixed schedules. We compared two-dose vaccine effectiveness (VE) by vaccine type (mRNA and/or ChAdOx1), interval between doses, and time since second dose in two of Canada's larger provinces.

Methods: Two-dose VE against SARS-CoV-2 infection or hospitalization among adults ≥18-years-old, including due to Alpha, Gamma and Delta variants of concern (VOC), was assessed at ≥14 days post-vaccination by test-negative design studies separately conducted in British Columbia and Quebec, Canada between May 30 and November 27 (epi-weeks 22-47), 2021.

Results: In both provinces, all homologous or heterologous mRNA and/or ChAdOx1 two-dose schedules were associated with ≥90% reduction in SARS-CoV-2 hospitalization risk for at least 7 months. With slight decline from a peak of >90%, VE against infection was ≥80% for at least 6 months following homologous mRNA vaccination, lower by ∼10% when both doses were ChAdOx1 but comparably-high following heterologous ChAdOx1 + mRNA receipt. Findings were similar by age group, sex and VOC. VE was significantly higher with longer 7-8-week vs. manufacturer-specified 3-4-week interval between mRNA doses.

Conclusions: Two doses of any mRNA and/or ChAdOx1 combination gave substantial and sustained protection against SARS-CoV-2 hospitalization, spanning Delta-dominant circulation. ChAdOx1 VE against infection was improved by heterologous mRNA series completion. A 7-8-week interval between first and second doses improved mRNA VE and may be the optimal schedule outside periods of intense epidemic surge. Findings support interchangeability and extended intervals between SARS-CoV-2 vaccine doses, with potential global implications for low-coverage areas and, going forward, for children.
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http://dx.doi.org/10.1093/cid/ciac290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9047203PMC
April 2022

O103 outbreak associated with minced celery among hospitalized individuals in Victoria, British Columbia, 2021.

Can Commun Dis Rep 2022 Jan 26;48(1):46-50. Epub 2022 Jan 26.

British Columbia Centres for Disease Control, Vancouver, BC.

Background: In April 2021, a Shiga toxin-producing () (STEC) O103 outbreak was identified among patients at two hospitals in Victoria, British Columbia (BC). The objective of this study is to describe this outbreak investigation and identify issues of food safety for high-risk products prepared for vulnerable populations.

Methods: Confirmed cases of O103 were reported to the Island Health communicable disease unit. The provincial public health laboratory conducted whole genome sequencing on confirmed case isolates, as per routine practice for STEC in BC. Exposure information was obtained through case interviews and review of hospital menus. Federal and local public health authorities conducted an inspection of the processing plant for the suspect source.

Results: Six confirmed cases of O103 were identified, all related by whole genome sequencing. The majority of cases were female (67%) and the median age was 61 years (range 24-87 years). All confirmed cases were inpatients or outpatients at two hospitals and were exposed to raw minced celery within prepared sandwiches provided by hospital food services. A local processor supplied the minced celery exclusively to the two hospitals. Testing of product at the processor was infrequent, and chlorine rinse occurred before mincing. The spread of residual . contamination through the mincing process, in addition to temperature abuse at the hospitals, are thought to have contributed to this outbreak.

Conclusion: Raw vegetables, such as celery, are a potential source of STEC and present a risk to vulnerable populations. Recommendations from this outbreak include more frequent testing at the processor, a review of the chlorination and mincing process and a review of hospital food services practices to mitigate temperature abuse.
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http://dx.doi.org/10.14745/ccdr.v48i01a07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8856827PMC
January 2022

Epidemiological analysis of the emergence and disappearance of the SARS-CoV-2 Kappa variant within a region of British Columbia, Canada.

Can Commun Dis Rep 2022 Jan 26;48(1):22-26. Epub 2022 Jan 26.

British Columbia Centre for Disease Control, Vancouver, BC.

Background: The Kappa variant is designated as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of interest (VOI). We identified 195 Kappa variant cases in a region of British Columbia, Canada-the largest published cluster in North America.

Objectives: To describe the epidemiology of the Kappa variant in relation to other circulating SARS-CoV-2 variants of concern (VOC) in the region to determine if the epidemiology of the Kappa variant supports a VOI or VOC status.

Methods: Clinical specimens testing positive for SARS-CoV-2 collected between March 10 and May 2, 2021, were screened for the detection of known circulating VOCs; approximately 50% of specimens were subsequently selected for whole genome sequencing (WGS). Epidemiological analysis was performed comparing the characteristics of Kappa cases to the main circulating variants in the region (Alpha and Gamma) and to non-VOC/VOI cases.

Results: A total of 2,079 coronavirus disease 2019 (COVID-19) cases were reported in the region during the study period, of which 54% were selected for WGS. The 1,131 sequenced cases were categorized into Kappa, Alpha, Gamma and non-VOC/VOI. While Alpha and Gamma cases were found to have a significantly higher attack rate among household contacts compared to non-VOI/VOC cases, Kappa was not.

Conclusion: Epidemiological analysis supports the designation of Kappa as a VOI and not a VOC. The Alpha and Gamma variants were found to be more transmissible, explaining their subsequent dominance in the region and the rapid disappearance of the Kappa variant. Variant surveillance strategies should focus on both detection of established VOCs and detection of potential new VOCs.
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http://dx.doi.org/10.14745/ccdr.v48i01a04DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8856721PMC
January 2022

Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in in Canada Using Staramr.

Microorganisms 2022 Jan 26;10(2). Epub 2022 Jan 26.

National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.

Whole genome sequencing (WGS) of supports both molecular typing and detection of antimicrobial resistance (AMR). Here, we evaluated the correlation between phenotypic antimicrobial susceptibility testing (AST) and in silico prediction of AMR from WGS in ( = 1321) isolated from human infections in Canada. Phenotypic AMR results from broth microdilution testing were used as the gold standard. To facilitate high-throughput prediction of AMR from genome assemblies, we created a tool called Staramr, which incorporates the ResFinder and PointFinder databases and a custom gene-drug key for antibiogram prediction. Overall, there was 99% concordance between phenotypic and genotypic detection of categorical resistance for 14 antimicrobials in 1321 isolates (18,305 of 18,494 results in agreement). We observed an average sensitivity of 91.2% (range 80.5-100%), a specificity of 99.7% (98.6-100%), a positive predictive value of 95.4% (68.2-100%), and a negative predictive value of 99.1% (95.6-100%). The positive predictive value of gentamicin was 68%, due to seven isolates that carried , which conferred MICs just below the breakpoint of resistance. Genetic mechanisms of resistance in these 1321 isolates included 64 unique acquired alleles and mutations in three chromosomal genes. In general, in silico prediction of AMR in was reliable compared to the gold standard of broth microdilution. WGS can provide higher-resolution data on the epidemiology of resistance mechanisms and the emergence of new resistance alleles.
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http://dx.doi.org/10.3390/microorganisms10020292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8875511PMC
January 2022

Comparative Single-Dose mRNA and ChAdOx1 Vaccine Effectiveness Against Severe Acute Respiratory Syndrome Coronavirus 2, Including Variants of Concern: Test-Negative Design, British Columbia, Canada.

J Infect Dis 2022 Aug;226(1):11-22

Public Health Laboratory, BC Centre for Disease Control, Vancouver, British Columbia, Canada.

Background: In British Columbia, Canada, most adults 50-69 years old became eligible for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine in April 2021, with chimpanzee adenoviral vectored vaccine (ChAdOx1) restricted to ≥55-year-olds and second doses deferred ≥6 weeks to optimize single-dose coverage.

Methods: Among adults 50-69 years old, single-dose messenger RNA (mRNA) and ChAdOx1 vaccine effectiveness (VE) against SARS-CoV-2 infection and hospitalization, including variant-specific, was assessed by test-negative design between 4 April and 2 October 2021.

Results: Single-dose VE included 11 861 cases and 99 544 controls. Median of postvaccination follow-up was 32 days (interquartile range, 15-52 days). Alpha, Gamma, and Delta variants comprised 23%, 18%, and 56%, respectively, of genetically characterized viruses. At 21-55 days postvaccination, single-dose mRNA and ChAdOx1 VE (95% confidence interval [CI]) was 74% (71%-76%) and 59% (53%-65%) against any infection and 86% (80%-90%) and 94% (85%-97%) against hospitalization, respectively. VE (95% CI) was similar against Alpha and Gamma infections for mRNA (80% [76%-84%] and 80% [75%-84%], respectively) and ChAdOx1 (69% [60%-76%] and 66% [56%-73%], respectively). mRNA VE was lower at 63% (95% CI, 56%-69%) against Delta but 85% (95% CI, 71%-92%) against Delta-associated hospitalization (nonestimable for ChAdOx1).

Conclusions: A single mRNA or ChAdOx1 vaccine dose gave important protection against SARS-CoV-2, including early variants of concern. ChAdOx1 VE was lower against infection, but 1 dose of either vaccine reduced the hospitalization risk by >85% to at least 8 weeks postvaccination. Findings inform program options, including longer dosing intervals.
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http://dx.doi.org/10.1093/infdis/jiac023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8807316PMC
August 2022

AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens.

BMC Genomics 2022 Jan 25;23(1):77. Epub 2022 Jan 25.

Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.

Background: Antibiotic resistance is a growing global health concern prompting researchers to seek alternatives to conventional antibiotics. Antimicrobial peptides (AMPs) are attracting attention again as therapeutic agents with promising utility in this domain, and using in silico methods to discover novel AMPs is a strategy that is gaining interest. Such methods can sift through large volumes of candidate sequences and reduce lab screening costs.

Results: Here we introduce AMPlify, an attentive deep learning model for AMP prediction, and demonstrate its utility in prioritizing peptide sequences derived from the Rana [Lithobates] catesbeiana (bullfrog) genome. We tested the bioactivity of our predicted peptides against a panel of bacterial species, including representatives from the World Health Organization's priority pathogens list. Four of our novel AMPs were active against multiple species of bacteria, including a multi-drug resistant isolate of carbapenemase-producing Escherichia coli.

Conclusions: We demonstrate the utility of deep learning based tools like AMPlify in our fight against antibiotic resistance. We expect such tools to play a significant role in discovering novel candidates of peptide-based alternatives to classical antibiotics.
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http://dx.doi.org/10.1186/s12864-022-08310-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8788131PMC
January 2022

A population-based analysis to determine the impact of the 13-valent pneumococcal conjugate vaccine on community-acquired pneumonia in British Columbia, Canada.

Vaccine 2022 02 7;40(7):1047-1053. Epub 2022 Jan 7.

Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver V6T 1Z3, Canada; School of Population and Public Health, Faculty of Medicine, The University of British Columbia, Vancouver, Canada. Electronic address:

Background: Pneumonia is a leading cause of morbidity and mortality globally. We determined the impact of 13-valent pneumococcal conjugate vaccine (PCV13) use on community-acquired pneumonia (CAP) rates eight years after the vaccine was introduced in the infant immunization program.

Methods: Using diagnostic codes from administrative databases, we calculated the overall and age-specific CAP incidence per month (2000-2018). Changes in the CAP incidence before and after the PCV13 vaccine program introduction were evaluated using negative binomial regression model adjusting for 7-valent pneumococcal conjugate vaccine program.

Results: The PCV13 vaccine infant immunization program was associated with declining CAP incidence among children aged 0-2 years (adjusted Incidence Rate Ratio (aIRR): 0.91; 95% CI: 0.87-0.96). Overall CAP incidence did not decrease in those aged 3-5 years (0.98; 95% CI: 0.93-1.04), 6-17 years (1.02; 95% CI: 0.97-1.08), 18-49 years (1.02; 95% CI:0.98-1.05), 50-64 years (1.07; 95% CI: 1.04-1.11), ≥65 years (1.05; 95% CI:1.02-1.08).

Conclusions: The PCV13 infant immunization program is temporally associated with a reduction in CAP incidence in vaccine target age group. However, no significant decrease in CAP incidence in other age groups warrants further study of the etiology of CAP to develop and implement effective prevention programs.
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http://dx.doi.org/10.1016/j.vaccine.2021.12.065DOI Listing
February 2022

Increasing Azithromycin Resistance in Neisseria gonorrhoeae Due to NG-MAST 12302 Clonal Spread in Canada, 2015 to 2018.

Antimicrob Agents Chemother 2022 03 3;66(3):e0168821. Epub 2022 Jan 3.

National Microbiology Laboratory, Public Health Agency of Canadagrid.415368.d, Winnipeg, Manitoba, Canada.

Azithromycin-resistant (AZIR) gonorrhea has been steadily increasing in Canada over the past decade, which is cause for alarm, as azithromycin (AZI) has been part of the combination therapy recommended by the Canadian Guidelines on Sexually Transmitted Infections (CGSTI) since 2012. Neisseria gonorrhoeae with AZI MICs ≥1 mg/L collected between 2015 and 2018 as part of the Gonococcal Antimicrobial Surveillance Program-Canada underwent antimicrobial susceptibility testing, molecular typing, and whole-genome sequencing. Regional, demographic, and clinical isolation site comparisons were made to aid in our understanding of AZI susceptibility trending. We identified 3,447 N. gonorrhoeae with AZI MICs of ≥1 mg/L in Canada, which increased from 6.3% in 2015 to 26.5% of isolates in 2018. Central Canada had the highest proportion, rising from 9.2% in 2015 to 31.2% in 2018. We identified 273 different N. gonorrhoeae multiantigen sequence types (NG-MAST) among these isolates, with ST-12302 the most prevalent (50.9%). Whole-genome sequencing identified the Neisseria lactamica-like mosaic locus as the mechanism of AZIR in isolates of ST-12302 and isolates genetically similar (differing by ≤5 bp), designated the ST-12302 genogroup, accounting for 65.2% of study isolates which were originally identified in central Canada but spread to other regions by 2018. Genomic analysis indicated that AZIR in Canadian N. gonorrhoeae expanded rapidly due to clonal spread of the ST-12302 genogroup. The rapid expansion of this AZIR clonal group in all regions of Canada is of concern. CGSTI are currently under review to address the increase in AZIR in Canada.
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http://dx.doi.org/10.1128/AAC.01688-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8923198PMC
March 2022

Four genomic clades of Candida auris identified in Canada, 2012-2019.

Med Mycol 2022 Jan;60(1)

National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada.

Candida auris is an emerging yeast that is associated with antifungal resistance and healthcare-associated outbreaks. From 2012 to 2019, there were 24 known cases of C. auris colonization or infection in Canada. Isolates were from axilla/groin (n = 6), ear (n = 5), blood (n = 4), toe (n = 2), and a variety of other sites (n = 7). Canadian isolates belonged to the four main genomic clades: Clade I (formerly called South Asian clade, n = 12), Clade II (East Asian, n = 3), Clade III (African, n = 4), and Clade IV (South American, n = 5). Isolates within each clade were clonal; however, whole genome sequencing may be helpful in identifying clusters within healthcare facilities.

Lay Summary: The fungal pathogen Candida auris has caused many hospital outbreaks and is often multidrug resistant. All four major strains of C. auris were identified in Canada from 2012 to 2019. Genomic epidemiology may be useful for identifying and reducing transmission of C. auris within hospitals.
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http://dx.doi.org/10.1093/mmy/myab079DOI Listing
January 2022

Population-based incidence of invasive pneumococcal disease in children and adults in Ontario and British Columbia, 2002-2018: A Canadian Immunization Research Network (CIRN) study.

Vaccine 2021 12 19;39(52):7545-7553. Epub 2021 Nov 19.

Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address:

Background: Invasive pneumococcal disease (IPD) burden, evaluated in Canada using reported confirmed cases in surveillance systems, is likely underestimated due to underreporting. We estimated the burden of IPD in Ontario and British Columbia (BC) by combining surveillance data with health administrative databases.

Methods: We established a cohort of 27,525 individuals in Ontario and BC. Laboratory-confirmed IPD cases were identified from Ontario's integrated Public Health Information System and the BC Centre for Disease Control Public Health Laboratory. Possible IPD cases were identified from hospitalization data in both provinces, and from emergency department visit data in Ontario. We estimated the age and sex adjusted annual incidence of IPD and pneumococcal conjugate/polysaccharide vaccine (PCV/PPV) serotype-specific IPD using Poisson regression models.

Results: In Ontario, 20,205 overall IPD cases, including 15,299 laboratory-confirmed cases, were identified with relatively stable age- and sex-adjusted annual incidence rates ranging from 13.7/100,000 (2005) to 13.6/100,000 (2018). In BC, 7,320 overall IPD cases, including 5,932 laboratory-confirmed cases were identified; annual incidence rates increased from 10.9/100,000 (2002) to 13.2/100,000 (2018). Older adults aged ≥ 85 years had the highest incidence rates. During 2007-2018 the incidence of PCV7 serotypes and additional PCV13 serotypes decreased while the incidence of unique PPV23 and non-vaccine serotypes increased in both provinces.

Conclusions: IPD continues to cause a substantial public health burden in Canada despite publicly funded pneumococcal vaccination programs, resulting in part from an increase in unique PPV23 and non-vaccine serotypes.
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http://dx.doi.org/10.1016/j.vaccine.2021.11.032DOI Listing
December 2021

Evaluation of observed and unobserved self-collection of saline gargle samples for the detection of SARS-CoV-2 in outpatients.

Diagn Microbiol Infect Dis 2022 Feb 2;102(2):115566. Epub 2021 Oct 2.

BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Division of Medical Microbiology, BC Children's Hospital & BC Women's Hospital & Health Centre, Vancouver, British Columbia, Canada. Electronic address:

The diagnostic sensitivity of observed and unobserved self-collected saline gargle samples for the molecular detection of SARS-CoV-2 in adults and school-aged children was evaluated against a reference standard of health care worker collected nasopharyngeal flocked swab. A total of 46 participants had a positive nasopharyngeal swab sample; of these, 10 were in the observed phase and 36 were in the unobserved phase. Only one matching saline gargle sample tested negative and this was in the unobserved phase, giving an overall sensitivity of 98%. Average viral target Ct values were higher in the saline gargle samples. RNaseP Ct values were lower in unobserved collected samples compared to observed collected samples. Unobserved self-collection of saline gargle samples is a promising outpatient testing method for COVID-19 diagnosis. The self-collection method has potential to simplify the diagnostic cycle and facilitate implementation of COVID-19 testing, particularly in settings with limited access to health care workers.
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http://dx.doi.org/10.1016/j.diagmicrobio.2021.115566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8486683PMC
February 2022

Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens.

Int J Infect Dis 2022 Jan 29;114:51-54. Epub 2021 Oct 29.

British Columbia Centre for Disease Control Public Health Laboratory, Provincial Health Services Authority, 655 West 12th Ave, Vancouver, British Columbia, Canada, V5Z 4R4. Electronic address:

Mutations in emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages can interfere with laboratory methods used to generate viral genome sequences for public health surveillance. We identified 20 mutations that are widespread in variant of concern lineages and affect widely used sequencing protocols by the ARTIC network and Freed et al. Three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada. We provide laboratory validation of protocol modifications that restored sequencing performance. The study findings indicate that genomic sequencing protocols require immediate updating to address emerging mutations. This work also suggests that routine monitoring and protocol updates will be necessary as SARS-CoV-2 continues to evolve. The bioinformatic and laboratory approaches used here provide guidance for this kind of assay maintenance.
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http://dx.doi.org/10.1016/j.ijid.2021.10.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8555373PMC
January 2022

Epizootiology of a Cryptococcus gattii outbreak in porpoises and dolphins from the Salish Sea.

Dis Aquat Organ 2021 Oct 21;146:129-143. Epub 2021 Oct 21.

The SeaDoc Society, Karen C. Drayer Wildlife Health Center - Orcas Island Office, UC Davis School of Veterinary Medicine, Eastsound, WA 98245, USA.

Cryptococcus gattii is a fungal pathogen that primarily affects the respiratory and nervous systems of humans and other animals. C. gattii emerged in temperate North America in 1999 as a multispecies outbreak of cryptococcosis in British Columbia (Canada) and Washington State and Oregon (USA), affecting humans, domestic animals, and wildlife. Here we describe the C. gattii epizootic in odontocetes. Cases of C. gattii were identified in 42 odontocetes in Washington and British Columbia between 1997 and 2016. Species affected included harbor porpoises Phocoena phocoena (n = 26), Dall's porpoises Phocoenoides dalli (n = 14), and Pacific white-sided dolphins Lagenorhynchus obliquidens (n = 2). The probable index case was identified in an adult male Dall's porpoise in 1997, 2 yr prior to the initial terrestrial outbreak. The spatiotemporal extent of the C. gattii epizootic was defined, and cases in odontocetes were found to be clustered around terrestrial C. gattii hotspots. Case-control analyses with stranded, uninfected odontocetes revealed that risk factors for infection were species (Dall's porpoises), age class (adult animals), and season (winter). This study suggests that mycoses are an emerging source of mortality for odontocetes, and that outbreaks may be associated with anthropogenic environmental disturbance.
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http://dx.doi.org/10.3354/dao03630DOI Listing
October 2021

Linear Regression Equations To Predict β-Lactam, Macrolide, Lincosamide, and Fluoroquinolone MICs from Molecular Antimicrobial Resistance Determinants in .

Antimicrob Agents Chemother 2022 01 18;66(1):e0137021. Epub 2021 Oct 18.

National Microbiology Laboratory, Public Health Agency of Canadagrid.415368.d, Winnipeg, Manitoba, Canada.

Antimicrobial resistance in Streptococcus pneumoniae represents a threat to public health, and monitoring the dissemination of resistant strains is essential to guiding health policy. Multiple-variable linear regression modeling was used to determine the contributions of molecular antimicrobial resistance determinants to antimicrobial MICs for penicillin, ceftriaxone, erythromycin, clarithromycin, clindamycin, levofloxacin, and trimethoprim-sulfamethoxazole. Training data sets consisting of Canadian S. pneumoniae isolates obtained from 1995 to 2019 were used to generate multiple-variable linear regression equations for each antimicrobial. The regression equations were then applied to validation data sets of Canadian ( = 439) and U.S. ( = 607 and  = 747) isolates. The MICs for β-lactam antimicrobials were fully explained by amino acid substitutions in motif regions of the penicillin binding proteins PBP1a, PPB2b, and PBP2x. Accuracies of predicted MICs within 1 doubling dilution to phenotypically determined MICs were 97.4% for penicillin, 98.2% for ceftriaxone, 94.8% for erythromycin, 96.6% for clarithromycin, 98.2% for clindamycin, 100% for levofloxacin, and 98.8% for trimethoprim-sulfamethoxazole, with an overall sensitivity of 95.8% and specificity of 98.0%. Accuracies of predicted MICs to the phenotypically determined MICs were similar to those of phenotype-only MIC comparison studies. The ability to acquire detailed antimicrobial resistance information directly from molecular determinants will facilitate the transition from routine phenotypic testing to whole-genome sequencing analysis and can fill the surveillance gap in an era of increased reliance on nucleic acid assay diagnostics to better monitor the dynamics of S. pneumoniae.
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http://dx.doi.org/10.1128/AAC.01370-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8765234PMC
January 2022

A One-Health Genomic Investigation of Gentamicin Resistance in Salmonella from Human and Chicken Sources in Canada, 2014 to 2017.

Antimicrob Agents Chemother 2021 11 27;65(12):e0096621. Epub 2021 Sep 27.

Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.

We investigated whether the increased prevalence of gentamicin resistance in Salmonella from human infections was related to a similar increased prevalence in isolates from broiler chickens and whether this increase may have been due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on gentamicin-resistant (Gen) Salmonella isolates from human and chicken sources collected from 2014 to 2017 by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). We determined the genomic relatedness of strains and characterized resistance genes and plasmids. From 2014 to 2017, 247 isolates of Gen Salmonella were identified by CIPARS: 188 were from humans, and 59 were from chicken sources (26 from live animals on farm and 33 from retail meat). The five most common Gen serovars were Salmonella enterica serovars Heidelberg ( = 93; 31.5%), 4,[5],12:i:- ( = 42; 14.2%), Kentucky ( = 37; 12.5%), Infantis ( = 33; 11.2%), and Typhimurium ( = 23; 7.8%). Phylogenomic analysis revealed that for Heidelberg and Infantis, there were closely related isolates from human and chicken sources. In both sources, resistance to gentamicin and spectinomycin was most frequently conferred by and '', respectively. Plasmid closure confirmed linkages of gentamicin and spectinomycin resistance genes and revealed instances of similar plasmids from both sources. Gentamicin and spectinomycin resistance genes were linked on the same plasmids, and some plasmids and isolates from humans and chickens were genetically similar, suggesting that the use of lincomycin-spectinomycin in chickens may be selecting for gentamicin-resistant Salmonella in broiler chickens and that these resistant strains may be acquired by humans.
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http://dx.doi.org/10.1128/AAC.00966-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8597779PMC
November 2021

Laboratory Exposures from an Unsuspected Case of Human Infection with Brucella canis.

Emerg Infect Dis 2021 09;27(9):2489-2491

We report a case of human infection with a Brucella canis isolate in an adult in Canada who was receiving a biologic immunomodulating medication. We detail subsequent investigations, which showed that 17 clinical microbiology staff had high-risk exposures to the isolate, 1 of whom had a positive result for B. canis.
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http://dx.doi.org/10.3201/eid2709.204701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8386805PMC
September 2021

Rapid Increase in SARS-CoV-2 P.1 Lineage Leading to Codominance with B.1.1.7 Lineage, British Columbia, Canada, January-April 2021.

Emerg Infect Dis 2021 11 13;27(11):2802-2809. Epub 2021 Aug 13.

Several severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) emerged in late 2020; lineage B.1.1.7 initially dominated globally. However, lineages B.1.351 and P.1 represent potentially greater risk for transmission and immune escape. In British Columbia, Canada, B.1.1.7 and B.1.351 were first identified in December 2020 and P.1 in February 2021. We combined quantitative PCR and whole-genome sequencing to assess relative contribution of VOCs in nearly 67,000 infections during the first 16 weeks of 2021 in British Columbia. B.1.1.7 accounted for <10% of screened or sequenced specimens early on, increasing to >50% by week 8. P.1 accounted for <10% until week 10, increased rapidly to peak at week 12, and by week 13 codominated within 10% of rates of B.1.1.7. B.1.351 was a minority throughout. This rapid expansion of P.1 but suppression of B.1.351 expands our understanding of population-level VOC patterns and might provide clues to fitness determinants for emerging VOCs.
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http://dx.doi.org/10.3201/eid2711.211190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8544957PMC
November 2021

Single-dose mRNA Vaccine Effectiveness Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Including Alpha and Gamma Variants: A Test-negative Design in Adults 70 Years and Older in British Columbia, Canada.

Clin Infect Dis 2022 04;74(7):1158-1165

BC Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada.

Background: Randomized-controlled trials of messenger RNA (mRNA) vaccine protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) included relatively few elderly participants. We assess single-dose mRNA vaccine effectiveness (VE) in adults ≥ 70 years old in British Columbia, Canada, where second doses were deferred by up to 16 weeks and where a spring 2021 wave uniquely included codominant circulation of Alpha (B.1.1.7) and Gamma (P.1) variants of concern (VOC).

Methods: Analyses included community-dwelling adults ≥ 70 years old with specimen collection between 4 April (epidemiological week 14) and 1 May (week 17) 2021. Adjusted VE was estimated by test-negative design. Cases were reverse-transcription polymerase chain reaction (RT-PCR) test-positive for SARS-CoV-2, and controls were test-negative. Vaccine status was defined by receipt of a single-dose ≥ 21 days before specimen collection, but a range of intervals was assessed. Variant-specific VE was estimated against viruses genetically characterized as Alpha, Gamma or non-VOC lineages.

Results: VE analyses included 16 993 specimens: 1226 (7%) test-positive cases and 15 767 test-negative controls. Of 1131 (92%) genetically characterized viruses, 509 (45%), 314 (28%), and 276 (24%) were Alpha, Gamma, and non-VOC lineages, respectively. At 0-13 days postvaccination, VE was negligible at 14% (95% confidence interval [CI], 0-26) but increased from 43% (95% CI, 30-53) at 14-20 days to 75% (95% CI, 63-83) at 35-41 days postvaccination. VE at ≥ 21 days postvaccination was 65% (95% CI, 58-71) overall: 72% (95% CI, 58-81), 67% (95% CI, 57-75), and 61% (95% CI, 45-72) for non-VOC, Alpha, and Gamma variants, respectively.

Conclusions: A single dose of mRNA vaccine reduced the risk of SARS-CoV-2 by about two-thirds in adults ≥ 70 years old, with protection only minimally reduced against Alpha and Gamma variants.
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http://dx.doi.org/10.1093/cid/ciab616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8406884PMC
April 2022

Diagnostic performance and clinical application of preoperative COVID-19 bedside testing with ID NOW™.

Can J Anaesth 2021 10 21;68(10):1569-1571. Epub 2021 May 21.

BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada.

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http://dx.doi.org/10.1007/s12630-021-02035-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8139543PMC
October 2021

Emergence of Harboring Metalloenzyme in Canada.

mSphere 2021 05 19;6(3). Epub 2021 May 19.

Antimicrobial Resistance & Nosocomial Infections, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.

In 2018 to 2019, PCR for carbapenemases in routine Gram-negative isolates submitted to the National Microbiology Laboratory revealed an increase in IMP-type metalloenzyme-positive isolates, mostly among Whole-genome sequencing revealed that 23 harbored within a chromosomal Tn element. Phylogenomics indicated diversity of isolates but also the presence of a few clonal isolates dispersed geographically. These isolates may be difficult to detect due to carbapenem susceptibility and false-negative results in phenotypic testing. Over the last decade or so, the frequency of isolation of clinical carbapenemase-producing organisms (CPOs) has increased among health care-associated infections. This may seriously compromise antimicrobial therapy, as carbapenems are considered the last line of defense against these organisms. The ability of carbapenemases to hydrolyze most β-lactams in addition to the co-occurrence of mechanisms of resistance to other classes of antimicrobials in CPOs can leave few options for treating infections. The class B metalloenzymes are globally distributed carbapenemases, and the most commonly found include the NDM, VIM, and IMP types. Our study describes a sudden emergence of IMP-27-harboring during 2018 to 2019 in Canada. There is a paucity of literature on IMP-27 isolates, and our data bolster the information on the genetic context, antimicrobial profiles, and phylogenomics of this group of CPOs.
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http://dx.doi.org/10.1128/mSphere.00048-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8265620PMC
May 2021

O121 outbreak associated with raw milk Gouda-like cheese in British Columbia, Canada, 2018.

Can Commun Dis Rep 2021 Jan 29;47(2):11-16. Epub 2021 Jan 29.

British Columbia Centre for Disease Control, Vancouver, BC.

Background: In 2018, a Shiga toxin-producing O121 outbreak that affected seven individuals was associated with raw milk Gouda-like cheese produced in British Columbia, Canada.

Objectives: To describe the . O121 outbreak investigation and recommend greater control measures for raw milk Gouda-like cheese.

Methods: Cases of . O121 were identified through laboratory testing results and epidemiologic surveillance data. The cases were interviewed on exposures of interest, which were analyzed against values for British Columbia. Environmental inspection of the dairy plant and the cheese products was conducted to ascertain a source of contamination. Whole genome multi-locus sequence typing (wgMLST) was performed on all positive . O121 clinical and food isolates at the provincial laboratory.

Results: Four out of the seven cases consumed the same raw milk Gouda-like cheese between August and October 2018. The implicated cheese was aged longer than the required minimum of 60 days, and no production deficiencies were noted. One sample of the implicated cheese tested positive for . O121. The seven clinical isolates and one cheese isolate matched by wgMLST within 6.5 alleles.

Conclusion: Raw milk Gouda and Gouda-like cheese has been implicated in three previous Shiga toxin-producing outbreaks in North America. It was recommended product labelling to increase consumer awareness and thermization of milk to decrease the risk of illness associated with raw milk Gouda and Gouda-like cheese.
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http://dx.doi.org/10.14745/ccdr.v47i01a03DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7972179PMC
January 2021

Self-Collected Saline Gargle Samples as an Alternative to Health Care Worker-Collected Nasopharyngeal Swabs for COVID-19 Diagnosis in Outpatients.

J Clin Microbiol 2021 03 19;59(4). Epub 2021 Mar 19.

Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.

We assessed the performance, stability, and user acceptability of swab-independent self-collected saliva and saline mouth rinse/gargle sample types for the molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in adults and school-aged children. Outpatients who had recently been diagnosed with COVID-19 or were presenting with suspected COVID-19 were asked to have a nasopharyngeal (NP) swab collected and provide at least one self-collected sample type. Participants were also asked about sample acceptability using a five-point Likert scale. For those previously diagnosed with COVID-19, all samples underwent real-time PCR testing using a lab-developed assay, and the majority were also tested using an FDA-authorized assay. For those presenting with suspected COVID-19, only those with a positive nasopharyngeal swab sample went on to have other samples tested. Saline mouth rinse/gargle and saliva samples were tested daily at time zero, day 1, and day 2 to assess nucleic acid stability at room temperature. Fifty participants (aged 4 to 71 years) were included; of these, 40 had at least one positive sample and were included in the primary sample yield analysis. Saline mouth rinse/gargle samples had a sensitivity of 98% (39/40), while saliva samples had a sensitivity of 79% (26/33). Both saline mouth rinse/gargle and saliva samples showed stable viral RNA detection after 2 days of room temperature storage. Mouth rinse/gargle samples had the highest (mean, 4.9) and health care worker (HCW)-collected NP swabs had the lowest acceptability scores (mean, 3.1). In conclusion, saline mouth rinse/gargle samples demonstrated higher combined user acceptability ratings and analytical performance than saliva and HCW-collected NP swabs. This sample type is a promising swab-independent option, particularly for outpatient self-collection in adults and school-aged children.
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http://dx.doi.org/10.1128/JCM.02427-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8092743PMC
March 2021

First reported outbreak of the emerging pathogen Candida auris in Canada.

Am J Infect Control 2021 06 21;49(6):804-807. Epub 2021 Jan 21.

Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Division of Medical Microbiology & Infection Control, Vancouver Coastal Health Authority, Vancouver, British Columbia, Canada. Electronic address:

Background: Candida auris was first described in Japan in 2009 and has since been detected in over 40 countries. The yeast is concerning for multiple reasons, primarily: (1) challenges with accurate identification; (2) reported multidrug resistance; (3) published mortality rates of 30%-60%; and (4) persistence in the environment associated with human transmission. We report the emergence of a healthcare-associated cluster in the Greater Vancouver area in 2018 and describe the measures implemented to contain its transmission.

Methods: Cases were identified through passive and ring surveillance of affected wards. Positive isolates were sent to provincial and national reference laboratories for confirmation and genomic characterization. Extensive infection control measures were implemented immediately after the initial case was identified.

Results: Four cases were identified during the outbreak. In a 4-month period, over 700 swabs were collected in order to screen 180 contacts. Whole genome sequencing concluded that all isolates clustered together and belonged to the South Asian clade. No isolates harbored FKS gene mutations associated with resistance to echinocandins. Infection control measures, including surveillance, education, cleaning and/or disinfection, patient cohorting, isolation, and hand hygiene, effectively contained the outbreak; it was declared over within 2 months.

Conclusions: The spread of C auris in healthcare facilities has not spared Canadian institutions. Our experience demonstrates that strict infection control measures combined with microbiological screening can effectively halt transmission in healthcare centers. The necessity of active prospective screening remains unclear.
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http://dx.doi.org/10.1016/j.ajic.2021.01.013DOI Listing
June 2021

Incidence of invasive pneumococcal disease after introduction of the 13-valent conjugate pneumococcal vaccine in British Columbia: A retrospective cohort study.

PLoS One 2020 30;15(9):e0239848. Epub 2020 Sep 30.

Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.

Background: A significant reduction in invasive pneumococcal disease (IPD) has been reported, across all ages, following the implementation of 7-valent conjugate pneumococcal vaccine (PCV7) globally, as part of infant immunization programs. We explored the additional impact of PCV13 on IPD over a 14-year period.

Methods: Using provincial laboratory surveillance and hospitalization data (N = 5791), we calculated the annual incidence of IPD following the implementation of PCV13 vaccine. Poisson regression was used to evaluate changes in the overall incidence of IPD, and serotype-specific IPD between PCV7 (2004-10) and PCV13 (2011-2015) eras.

Results: Overall, IPD rates have seen a modest decline in the PCV13 compared to the PCV7 era (IRR 0.84; 95% CI: 0.79-0.89); this was seen in children ≤2 years of age, and the majority of the adult cohort. Rates of vaccine-type IPD (PCV7 and PCV13) also decreased in the PCV13 era. In contrast, IPD incidence related to non-PCV13 (IRR: 1.56; 95%CI:1.43-1.72) and non-vaccine serotypes (IRR: 2.12; 95%CI:1.84-2.45) increased in the PCV13 era compared to the PCV7 era.

Conclusions: A modest reduction in IPD from the PCV13 vaccine was observed, with gains limited to the immunized cohort and adults. However, a significant increase in non-vaccine serotypes emphasizes the need for continued surveillance.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239848PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526878PMC
December 2020
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