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1.
BMC Infect Dis ; 24(1): 147, 2024 Jan 30.
Article in English | MEDLINE | ID: mdl-38291361

ABSTRACT

BACKGROUND: Influenza and RSV coinfections are not commonly seen but are concerning as they can lead to serious illness and adverse clinical outcomes among vulnerable populations. Here we describe the clinical features and outcomes of influenza and RSV coinfections in hospitalized adults. METHODS: A cohort study was performed with pooled active surveillance in hospitalized adults ≥ 50 years from the Serious Outcomes Surveillance Network of the Canadian Immunization Research Network (CIRN SOS) during the 2012/13, 2013/14, and 2014/15 influenza seasons. Descriptive statistics summarized the characteristics of influenza/RSV coinfections. Kaplan-Meier estimated the probability of survival over the first 30 days of hospitalization. RESULTS: Over three influenza seasons, we identified 33 cases of RSV and influenza coinfection, accounting for 2.39 cases per 1,000 hospitalizations of patients with acute respiratory illnesses. Adults aged 50 + years commonly reported cough (81.8%), shortness of breath (66.7%), sputum production (45.5%), weakness (33.3%), fever (27.3%), and nasal congestion (24.2%) as constitutional and lower respiratory tract infection symptoms. The mortality rate was substantial (12.1%), and age, comorbidity burden, and frailty were associated with a higher risk for adverse clinical outcomes. CONCLUSIONS: Older adults are at higher risk for complications from influenza and RSV coinfections, especially those over 65 with a high comorbidity burden and frailty.


Subject(s)
Coinfection , Frailty , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Humans , Aged , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Influenza, Human/diagnosis , Respiratory Syncytial Virus Infections/diagnosis , Coinfection/epidemiology , Cohort Studies , Canada/epidemiology , Hospitalization , Vaccination , Risk Factors
2.
Emerg Infect Dis ; 29(1): 175-178, 2023 01.
Article in English | MEDLINE | ID: mdl-36573611

ABSTRACT

Whole blood is the optimal specimen for anaplasmosis diagnosis but might not be available in all cases. We PCR tested serum samples collected in Canada for Anaplasma serology and found 84.8%-95.8% sensitivity and 2.8 average cycle threshold elevation. Serum can be acceptable for detecting Anaplasma spp. when whole blood is unavailable.


Subject(s)
Anaplasma phagocytophilum , Anaplasmosis , Animals , Humans , Anaplasmosis/diagnosis , Real-Time Polymerase Chain Reaction , Anaplasma phagocytophilum/genetics , Canada/epidemiology
3.
Clin Microbiol Rev ; 34(3)2021 06 16.
Article in English | MEDLINE | ID: mdl-33980687

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19 Serological Testing/methods , COVID-19/diagnostic imaging , COVID-19/diagnosis , SARS-CoV-2/genetics , Biosensing Techniques , Genome, Viral/genetics , Humans , Nucleic Acid Amplification Techniques/methods , Point-of-Care Testing , SARS-CoV-2/immunology , Specimen Handling/methods
4.
Emerg Infect Dis ; 28(6): 1292-1294, 2022 06.
Article in English | MEDLINE | ID: mdl-35608954

ABSTRACT

In July 2021, a PCR-confirmed case of locally acquired Babesia microti infection was reported in Atlantic Canada. Clinical features were consistent with babesiosis and resolved after treatment. In a region where Lyme disease and anaplasmosis are endemic, the occurrence of babesiosis emphasizes the need to enhance surveillance of tickborne infections.


Subject(s)
Anaplasma phagocytophilum , Anaplasmosis , Babesia microti , Babesiosis , Borrelia burgdorferi , Ixodes , Lyme Disease , Anaplasmosis/diagnosis , Anaplasmosis/drug therapy , Anaplasmosis/epidemiology , Animals , Babesiosis/diagnosis , Babesiosis/drug therapy , Babesiosis/epidemiology , Canada/epidemiology , Lyme Disease/diagnosis , Lyme Disease/epidemiology
5.
J Infect Dis ; 222(3): 428-437, 2020 07 06.
Article in English | MEDLINE | ID: mdl-32147711

ABSTRACT

BACKGROUND: We examined frailty as a predictor of recovery in older adults hospitalized with influenza and acute respiratory illness. METHODS: A total of 5011 patients aged ≥65 years were admitted to Canadian Serious Outcomes Surveillance Network hospitals during the 2011/2012, 2012/2013, and 2013/2014 influenza seasons. Frailty was measured using a previously validated frailty index (FI). Poor recovery was defined as death by 30 days postdischarge or an increase of more than 0.06 (≥2 persistent new health deficits) on the FI. Multivariable logistic regression controlled for age, sex, season, influenza diagnosis, and influenza vaccination status. RESULTS: Mean age was 79.4 (standard deviation = 8.4) years; 53.1% were women. At baseline, 15.0% (n = 750) were nonfrail, 39.3% (n = 1971) were prefrail, 39.8% (n = 1995) were frail, and 5.9% (n = 295) were most frail. Poor recovery was experienced by 21.4%, 52.0% of whom had died. Frailty was associated with lower odds of recovery in all 3 seasons: 2011/2012 (odds ratio [OR] = 0.70; 95% confidence interval [CI], 0.59-0.84), 2012/2013 (OR = 0.72; 95% CI, 0.66-0.79), and 2013/2014 (OR = 0.75; 95% CI, 0.69-0.82); results varied by season, influenza status, vaccination status, and age. CONCLUSIONS: Increasing frailty is associated with lower odds of recovery, and persistent worsening frailty is an important adverse outcome of acute illness.


Subject(s)
Frailty/diagnosis , Geriatric Assessment/methods , Influenza, Human/complications , Respiratory Tract Diseases/complications , Acute Disease , Aged , Aged, 80 and over , Canada/epidemiology , Female , Frailty/mortality , Hospitalization , Humans , Influenza, Human/epidemiology , Logistic Models , Male , Multivariate Analysis , Respiratory Tract Diseases/epidemiology , Time Factors
6.
J Clin Microbiol ; 58(7)2020 06 24.
Article in English | MEDLINE | ID: mdl-32321781

ABSTRACT

Compared to the standard two-tiered testing (STTT) algorithm for Lyme disease serology using an enzyme immunoassay (EIA) followed by Western blotting, data from the United States suggest that a modified two-tiered testing (MTTT) algorithm employing two EIAs has improved sensitivity to detect early localized Borrelia burgdorferi infections without compromising specificity. From 2011 to 2014, in the Canadian province of Nova Scotia, where Lyme disease is hyperendemic, sera submitted for Lyme disease testing were subjected to a whole-cell EIA, followed by C6 EIA and subsequently IgM and/or IgG immunoblots on sera with EIA-positive or equivocal results. Here, we evaluate the effectiveness of the MTTT algorithm compared to the STTT approach in a Nova Scotian population. Retrospective chart reviews were performed on patients testing positive with the whole-cell and C6 EIAs (i.e., the MTTT algorithm). Patients were classified as having Lyme disease if they had a positive STTT result, a negative STTT result but symptoms consistent with Lyme disease, or evidence of seroconversion on paired specimens. Of the 10,253 specimens tested for Lyme disease serology, 9,806 (95.6%) were negative. Of 447 patients who tested positive, 271 charts were available for review, and 227 were classified as patients with Lyme disease. The MTTT algorithm detected 25% more early infections with a specificity of 99.56% (99.41 to 99.68%) compared to the STTT. These are the first Canadian data to show that serology using a whole-cell sonicate EIA followed by a C6 EIA (MTTT) had improved sensitivity for detecting early B. burgdorferi infection with specificity similar to that of two-tiered testing using Western blots.


Subject(s)
Borrelia burgdorferi , Lyme Disease , Algorithms , Antibodies, Bacterial , Humans , Immunoenzyme Techniques , Immunoglobulin M , Lyme Disease/diagnosis , Nova Scotia , Retrospective Studies , Sensitivity and Specificity , Serologic Tests
7.
Mol Microbiol ; 108(5): 536-550, 2018 06.
Article in English | MEDLINE | ID: mdl-29509331

ABSTRACT

Enteropathogenic Escherichia coli (EPEC) use a type 3 secretion system (T3SS) for injection of effectors into host cells and intestinal colonization. Here, we demonstrate that the multicargo chaperone CesT has two strictly conserved tyrosine phosphosites, Y152 and Y153 that regulate differential effector secretion in EPEC. Conservative substitution of both tyrosine residues to phenylalanine strongly attenuated EPEC type 3 effector injection into host cells, and limited Tir effector mediated intimate adherence during infection. EPEC expressing a CesT Y152F variant were deficient for NleA effector expression and exhibited significantly reduced translocation of NleA into host cells during infection. Other effectors were observed to be dependent on CesT Y152 for maximal translocation efficiency. Unexpectedly, EPEC expressing a CesT Y153F variant exhibited significantly enhanced effector translocation of many CesT-interacting effectors, further implicating phosphosites Y152 and Y153 in CesT functionality. A mouse infection model of intestinal disease using Citrobacter rodentium revealed that CesT tyrosine substitution variants displayed delayed colonization and were more rapidly cleared from the intestine. These data demonstrate genetically separable functions for tandem tyrosine phosphosites within CesT. Therefore, CesT via its C-terminal tyrosine phosphosites, has relevant roles beyond typical type III secretion chaperones that interact and stabilize effector proteins.


Subject(s)
Enteropathogenic Escherichia coli/pathogenicity , Escherichia coli Infections/microbiology , Escherichia coli Proteins/metabolism , Molecular Chaperones/metabolism , Organophosphates/metabolism , Polymers/metabolism , Virulence Factors/metabolism , Animals , Disease Models, Animal , Enteropathogenic Escherichia coli/genetics , Escherichia coli O157 , Escherichia coli Proteins/genetics , Female , HeLa Cells , Humans , Intestinal Diseases/microbiology , Mice , Mice, Inbred C57BL , Molecular Chaperones/genetics , Tyrosine/genetics , Virulence/genetics , Virulence Factors/genetics
8.
Plasmid ; 98: 45-51, 2018 06.
Article in English | MEDLINE | ID: mdl-30217467

ABSTRACT

BACKGROUND: Serotyping of Streptococcus pneumoniae is an integral part of disease surveillance, with over 92 serotypes characterized to date using traditional serotyping. To identify the most predominant disease causing serotypes, molecular serotyping methods are now increasingly being used, like conventional and real-time multiplex PCR (cmPCR and rmPCR, respectively). Given that cmPCR consists of eight reactions spanning 41 targets, and rmPCR consists of seven triplex reactions, standardizing positive controls for these assays is challenging. As such, a 43-target plasmid for cmPCR (pSpn-CM1) and a 23 target plasmid for rmPCR (pSpn-RM1) were designed and validated. METHODS: Plasmid pSpn-RM1 was designed and synthesized as chimeric DNA sequences to include all PCR target primer binding sites sequences for cmPCR. Plasmid pSpn-RM1 consisted of all primer and probe sequences required for rmPCR. Additional targets (lytA and cpsA) were included in both plasmids for quantification, following their propagation and purification from Escherichia coli. RESULTS: When tested using the cmPCR reactions, all targets could be reproducibly be detected using pSpn-CM1 as template, with good amplicon visibility at a concentration of 1.4 (± 0.3) × 105 copies/ml was used. For the rmPCR reactions, all targets were reproducibly amplified with a concentration of 1.1 (± 0.2) × 104 copies/ml of pSpn-RM1, and the PCR efficiency for each target was equivalent to DNA extracted from representative S. pneumoniae serotypes. CONCLUSIONS: These quantifiable multi-target plasmids simplify the preparation of controls for PCR-based serotyping of S. pneumoniae, and methods herein could be extended to other highly multiplexed PCR assays.


Subject(s)
Bacterial Typing Techniques/methods , Multiplex Polymerase Chain Reaction/methods , Plasmids/genetics , Pneumococcal Infections/diagnosis , Quality Control , Real-Time Polymerase Chain Reaction/methods , Streptococcus pneumoniae/classification , DNA, Bacterial , High-Throughput Screening Assays , Humans , Pneumococcal Infections/microbiology , Pneumococcal Infections/prevention & control , Streptococcus pneumoniae/genetics , Streptococcus pneumoniae/isolation & purification
9.
J Infect Dis ; 216(4): 405-414, 2017 08 15.
Article in English | MEDLINE | ID: mdl-28931244

ABSTRACT

Background: Influenza is an important cause of morbidity and mortality among older adults. Even so, effectiveness of influenza vaccine for older adults has been reported to be lower than for younger adults, and the impact of frailty on vaccine effectiveness (VE) and outcomes is uncertain. We aimed to study VE against influenza hospitalization in older adults, focusing on the impact of frailty. Methods: We report VE of trivalent influenza vaccine (TIV) in people ≥65 years of age hospitalized during the 2011-2012 influenza season using a multicenter, prospective, test-negative case-control design. A validated frailty index (FI) was used to measure frailty. Results: Three hundred twenty cases and 564 controls (mean age, 80.6 and 78.7 years, respectively) were enrolled. Cases had higher baseline frailty than controls (P = .006). In the fully adjusted model, VE against influenza hospitalization was 58.0% (95% confidence interval [CI], 34.2%-73.2%). The contribution of frailty was important; adjusting for frailty alone yielded a VE estimate of 58.7% (95% CI, 36.2%-73.2%). VE was 77.6% among nonfrail older adults and declined as frailty increased. Conclusions: Despite commonly held views that VE is poor in older adults, we found that TIV provided good protection against influenza hospitalization in older adults who were not frail, though VE diminished as frailty increased. Clinical Trials Registration: NCT01517191.


Subject(s)
Frail Elderly , Hospitalization/statistics & numerical data , Influenza Vaccines/therapeutic use , Influenza, Human/prevention & control , Vaccine Potency , Aged , Aged, 80 and over , Case-Control Studies , Female , Humans , Influenza Vaccines/administration & dosage , Intensive Care Units , Logistic Models , Male , Prospective Studies , Seasons , Treatment Outcome
10.
J Bacteriol ; 199(5)2017 03 01.
Article in English | MEDLINE | ID: mdl-27994017

ABSTRACT

Nominally an environmental organism, Legionella pneumophila is an intracellular parasite of protozoa but is also the causative agent of the pneumonia termed Legionnaires' disease, which results from inhalation of aerosolized bacteria by susceptible humans. Coordination of gene expression by a number of identified regulatory factors, including OxyR, assists L. pneumophila in adapting to the stresses of changing environments. L. pneumophila OxyR (OxyRLp) is an ortholog of Escherichia coli OxyR; however, OxyRLp was shown elsewhere to be functionally divergent, such that it acts as a transcription regulator independently of the oxidative stress response. In this study, the use of improved gene deletion methods has enabled us to generate an unmarked in-frame deletion of oxyR in L. pneumophila Lack of OxyRLp did not affect in vitro growth or intracellular growth in Acanthamoeba castellanii protozoa and U937-derived macrophages. The expression of OxyRLp does not appear to be regulated by CpxR, even though purified recombinant CpxR bound a DNA sequence similar to that reported for CpxR elsewhere. Surprisingly, a lack of OxyRLp resulted in elevated activity of the promoters located upstream of icmR and the lpg1441-cpxA operon, and OxyRLp directly bound to these promoter regions, suggesting that OxyRLp is a direct repressor. Interestingly, a strain overexpressing OxyRLp demonstrated reduced intracellular growth in A. castellanii but not in U937-derived macrophages, suggesting that balanced expression control of the two-component CpxRA system is necessary for survival in protozoa. Taken together, this study suggests that OxyRLp is a functionally redundant transcriptional regulator in L. pneumophila under the conditions evaluated herein.IMPORTANCELegionella pneumophila is an environmental pathogen, with its transmission to the human host dependent upon its ability to replicate in protozoa and survive within its aquatic niche. Understanding the genetic factors that contribute to L. pneumophila survival within each of these unique environments will be key to limiting future point-source outbreaks of Legionnaires' disease. The transcriptional regulator L. pneumophila OxyR (OxyRLp) has been previously identified as a potential regulator of virulence traits warranting further investigation. This study demonstrated that oxyR is nonessential for L. pneumophila survival in vitro and in vivo via mutational analysis. While the mechanisms of how OxyRLp expression is regulated remain elusive, this study shows that OxyRLp negatively regulates the expression of the cpxRA two-component system necessary for intracellular survival in protozoa.


Subject(s)
Bacterial Proteins/metabolism , Gene Expression Regulation, Bacterial/physiology , Legionella pneumophila/metabolism , Repressor Proteins/metabolism , Transcription Factors/metabolism , Acanthamoeba castellanii/microbiology , Bacterial Proteins/genetics , Humans , Legionella pneumophila/genetics , Macrophages/microbiology , Mutation , Repressor Proteins/genetics , Transcription Factors/genetics , U937 Cells
11.
Mol Microbiol ; 99(2): 236-53, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26395460

ABSTRACT

Recently, we identified a novel disulfide oxidoreductase, SdbA, in the oral bacterium Streptococcus gordonii. Disulfide oxidoreductases form disulfide bonds in nascent proteins using a CXXC catalytic motif. Typically, the N-terminal cysteine interacts with substrates, whereas the C-terminal cysteine is buried and only reacts with the first cysteine of the motif. In this study, we investigated the SdbA C(86) P(87) D(88) C(89) catalytic motif. In vitro, SdbA single cysteine variants at the N or C-terminal position (SdbAC86P and SdbAC89A ) were active but displayed different susceptibility to oxidation, and N-terminal cysteine was prone to sulfenylation. In S. gordonii, mutants with a single N-terminal cysteine were inactive and formed unstable disulfide adducts with other proteins. Activity was partially restored by inactivation of pyruvate oxidase, a hydrogen peroxide generator. Presence of the C-terminal cysteine alone (in the SdbAC86P variant) could complement the ΔsdbA mutant and restore disulfide bond formation in recombinant and natural protein substrates. These results provide evidence that certain disulfide oxidoreductases can catalyze disulfide bond formation using a single cysteine of the CXXC motif, including the buried C-terminal cysteine.


Subject(s)
Bacterial Proteins/metabolism , Cysteine/metabolism , Disulfides/metabolism , Oxidoreductases/metabolism , Streptococcus gordonii/enzymology , Amino Acid Motifs , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Biocatalysis , Catalytic Domain , Cysteine/chemistry , Cysteine/genetics , Disulfides/chemistry , Oxidoreductases/chemistry , Oxidoreductases/genetics , Protein Structure, Tertiary , Streptococcus gordonii/chemistry , Streptococcus gordonii/genetics
12.
BMC Infect Dis ; 17(1): 805, 2017 12 29.
Article in English | MEDLINE | ID: mdl-29284435

ABSTRACT

BACKGROUND: The Serious Outcomes Surveillance (SOS) Network was established to monitor seasonal influenza complications among hospitalized Canadian adults and to assess the effectiveness of influenza vaccination against severe outcomes. Here we report age- and strain-specific vaccine effectiveness (VE) in preventing severe outcomes during a season characterized by mixed outbreaks of four different influenza strains. METHODS: This prospective, multicentre, test-negative case-control study evaluated the VE of trivalent influenza vaccine (TIV) in the prevention of laboratory-confirmed influenza-hospitalization in adults aged ≥16 years (all adults) and adults aged 16-64 years (younger adults). The SOS Network identified hospitalized patients with diagnoses potentially attributable to influenza during the 2011/12 influenza season. Swabs collected at admission were tested by reverse transcriptase polymerase chain reaction (RT PCR) or viral culture to discriminate influenza cases (positive) from controls (negative). VE was calculated as 1-odds ratio (OR) of vaccination in cases versus controls × 100. RESULTS: Overall, in all adults, the unadjusted and adjusted VEs of TIV against influenza-hospitalization were 41.8% (95% Confidence Interval [CI]: 26.0, 54.3), and 42.8% (95% CI: 23.8, 57.0), respectively. In younger adults (16-64 years), the unadjusted and adjusted VEs of TIV against influenza-hospitalization were 35.8% (95% CI: 4.5, 56.8) and 33.2% (95% CI: -6.7, 58.2), respectively. In the all adults group, adjusted VE against influenza A/H1N1 was 72.5% (95% CI: 30.5, 89.1), against A/H3N2 was 86.1% (95% CI: 40.1, 96.8), against B/Victoria was 40.5% (95% CI: -28.9, 72.6), and against B/Yamagata was 32.3% (95% CI: -8.3, 57.7). The adjusted estimate of early season VE (from November 1 to March 11) was 54.4% (95% CI: 29.7-70.4), which was higher than late season (from March 11 to May 25) VE estimate (VE: 29.7%, 95% CI: -5.3, 53.1). CONCLUSIONS: These results suggest that TIV was highly effective against A viruses and moderately effective against B viruses during a mild season characterised by co-circulation of four influenza strains in Canada. Findings underscore the need to provide VE assessment by subtype/lineage as well as the timing of vaccination (early season vs late season) to accurately evaluate vaccine performance and thus guide public health decision-making. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01517191. Registration was retrospective and the date of registration was January 17, 2012.


Subject(s)
Influenza Vaccines , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Adolescent , Adult , Aged , Canada/epidemiology , Case-Control Studies , Disease Outbreaks , Female , Hospitalization/statistics & numerical data , Humans , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza A Virus, H3N2 Subtype/immunology , Influenza A Virus, H3N2 Subtype/pathogenicity , Influenza B virus/immunology , Influenza B virus/pathogenicity , Influenza Vaccines/immunology , Influenza Vaccines/therapeutic use , Influenza, Human/virology , Male , Middle Aged , Odds Ratio , Prospective Studies , Seasons , Vaccination , Young Adult
13.
Can J Infect Dis Med Microbiol ; 2016: 1280247, 2016.
Article in English | MEDLINE | ID: mdl-27366155

ABSTRACT

Background. Norovirus is the leading cause of viral gastroenteritis, with GII.4 being the most common circulating genotype. Recently, outbreaks in China revealed that norovirus GII.17 GII.P17 had become predominant. Objective. This study aimed to characterize the distribution of norovirus genotypes circulating in Nova Scotia. Methods. Stool specimens were collected from gastrointestinal outbreaks in Nova Scotia between Jan 2014 and June 2015 and subjected to real-time RT-PCR. Norovirus-positive specimens were referred to the National Microbiology Laboratory for sequence-based genotyping. Results. The first norovirus GII.P17-GII.17 outbreak in Canada was identified, but no widespread activity was observed in Nova Scotia. Discussion. It is unknown whether GII.P17-GII.17 is more widespread in Canada since contributions to Canadian surveillance are too sparse to effectively monitor the epidemiology of emerging norovirus genotypes. Conclusions. Presence of norovirus GII.17:P17 in Canada highlights the need for more systematic surveillance to ensure that molecular targets used for laboratory detection are effective and help understand norovirus evolution, epidemiology, and pathogenesis.

14.
J Clin Microbiol ; 53(5): 1748-51, 2015 May.
Article in English | MEDLINE | ID: mdl-25740765

ABSTRACT

The recent emergence of a severe respiratory disease caused by enterovirus D68 prompted investigation into whether Canadian hospital and provincial laboratories can detect this virus using commercial and laboratory-developed assays. This study demonstrated analytical sensitivity differences between commercial and laboratory-developed assays for the detection of enterovirus D68.


Subject(s)
Clinical Laboratory Techniques/methods , Diagnostic Tests, Routine/methods , Enterovirus D, Human/isolation & purification , Enterovirus Infections/diagnosis , Laboratory Proficiency Testing , Respiratory Tract Infections/diagnosis , Canada , Enterovirus Infections/virology , Humans , Respiratory Tract Infections/virology , Sensitivity and Specificity
15.
J Clin Microbiol ; 52(6): 2186-8, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24696023

ABSTRACT

The Viper HSV-Q(x) assay was evaluated for the detection of herpes simplex virus 1 (HSV-1) and HSV-2 in specimens from oral, anogenital, and other miscellaneous sites. The HSV-Q(x) assay was found to be highly sensitive and accurate; however, a gray zone may be required for specimens with values falling between 50 and 800 maximum relative fluorescence units.


Subject(s)
Herpes Genitalis/diagnosis , Herpes Genitalis/virology , Herpes Simplex/diagnosis , Herpes Simplex/virology , Molecular Diagnostic Techniques/methods , Simplexvirus/classification , Simplexvirus/isolation & purification , Fluorescence , Genitalia/virology , Humans , Molecular Diagnostic Techniques/standards , Mouth/virology , Sensitivity and Specificity
16.
Virol J ; 11: 129, 2014 Jul 18.
Article in English | MEDLINE | ID: mdl-25037234

ABSTRACT

BACKGROUND: Although national surveillance programs are in place to monitor norovirus epidemiology, the emergence of new strains and the genetic diversity among genotypes can be challenging for clinical laboratories. This study evaluated the analytical and clinical performance characteristics of one real-time RT-PCR and two end-point RT-PCRs commonly used in microbiology laboratories. METHODS: Lower limit of detection (LoD) was determined using 10-fold dilutions of noroviruses belonging to different genotypes. The clinical performance of the real-time and end-point RT-PCRs was assessed in parallel using nucleic acids extracted from 186 stool specimens. RESULTS: The real-time RT-PCR was highly sensitive and specific for the detection of norovirus genotypes that are currently circulating in Canada. In contrast, the two end-point RT-PCRs displayed poor analytical sensitivity or complete failure to detect certain norovirus genotypes, which was correlated to sequence mismatches in the primer-binding sites. In an attempt to improve norovirus detection with the end-point RT-PCRs, both assays were processed concurrently and detection from either assay was considered a positive result. Concurrent testing resulted in only a modest increase in clinical sensitivity (75.0%) compared to each assay alone (62.5% and 71.9%). However, the false positivity rate increased from 1.98% and 3.36% for the assays alone to 5.47% with concurrent testing. CONCLUSIONS: This study emphasizes the benefits of a real-time method and provides support for routine surveillance to monitor norovirus epidemiology and ongoing proficiency testing to ensure detection of circulating norovirus genotypes.


Subject(s)
Caliciviridae Infections/diagnosis , Caliciviridae Infections/virology , Gastroenteritis/diagnosis , Gastroenteritis/virology , Genotype , Norovirus/genetics , Humans , Real-Time Polymerase Chain Reaction , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity
17.
Sci Rep ; 14(1): 18378, 2024 08 08.
Article in English | MEDLINE | ID: mdl-39112632

ABSTRACT

We developed and validated the Influenza Severity Scale (ISS), a standardized risk assessment for influenza, to estimate and predict the probability of major clinical events in patients with laboratory-confirmed infection. Data from the Canadian Immunization Research Network's Serious Outcomes Surveillance Network (2011/2012-2018/2019 influenza seasons) enabled the selecting of all laboratory-confirmed influenza patients. A machine learning-based approach then identified variables, generated weighted scores, and evaluated model performance. This study included 12,954 patients with laboratory-confirmed influenza infections. The optimal scale encompassed ten variables: demographic (age and sex), health history (smoking status, chronic pulmonary disease, diabetes mellitus, and influenza vaccination status), clinical presentation (cough, sputum production, and shortness of breath), and function (need for regular support for activities of daily living). As a continuous variable, the scale had an AU-ROC of 0.73 (95% CI, 0.71-0.74). Aggregated scores classified participants into three risk categories: low (ISS < 30; 79.9% sensitivity, 51% specificity), moderate (ISS ≥ 30 but < 50; 54.5% sensitivity, 55.9% specificity), and high (ISS ≥ 50; 51.4% sensitivity, 80.5% specificity). ISS demonstrated a solid ability to identify patients with hospitalized laboratory-confirmed influenza at increased risk for Major Clinical Events, potentially impacting clinical practice and research.


Subject(s)
Influenza, Human , Severity of Illness Index , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Male , Canada/epidemiology , Female , Middle Aged , Adult , Aged , Risk Assessment/methods , Young Adult , Adolescent
18.
Viruses ; 16(8)2024 Aug 10.
Article in English | MEDLINE | ID: mdl-39205254

ABSTRACT

Despite the provision of a mumps vaccination program in Canada for over three decades, mumps has not reached elimination. Instead, a re-emergence has been observed in vaccinated populations, particularly in young adults. These outbreaks have been almost exclusively due to genotype G infections, a trend that has been seen in other countries with high mumps vaccination rates. To characterize mumps outbreaks in Canada, genomes from samples from Manitoba (n = 209), Newfoundland (n = 25), and Nova Scotia (n = 48) were sequenced and analysed by Bayesian inference. Whole genome sequencing was shown to be highly discriminatory for outbreak investigations compared to traditional Sanger sequencing. The results showed that mumps virus genotype G most likely circulated endemically in Canada and between Canada and the US. Overall, this Canadian outbreak data from different provinces and ancestral strains demonstrates the benefits of molecular genomic data to better characterize mumps outbreaks, but also suggests genomics could further our understanding of the reasons for potential immune escape of mumps genotype G and evolution in highly vaccinated populations. With a possible endemic circulation of mumps genotype G and the remaining risk of new imported cases, increased surveillance and alternative vaccination strategies may be required for Canada to reach the current target for mumps or a future elimination status.


Subject(s)
Disease Outbreaks , Genome, Viral , Genotype , Mumps virus , Mumps , Phylogeny , Mumps/epidemiology , Mumps/virology , Mumps/transmission , Humans , Canada/epidemiology , Mumps virus/genetics , Mumps virus/classification , Mumps virus/isolation & purification , Adult , Young Adult , Male , Adolescent , Female , Child , Whole Genome Sequencing , Genomics/methods , Middle Aged , Child, Preschool , Endemic Diseases , Infant , Bayes Theorem
19.
Microbiol Spectr ; 12(6): e0359323, 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38682930

ABSTRACT

Lyme arthritis can present similarly to other causes of joint pain and swelling including septic arthritis and other acute and chronic arthropathies of childhood. Septic arthritis, although rare, constitutes an orthopedic emergency and requires early surgical intervention to reduce the risk of permanent joint damage. Currently, results of standard serologic tests to diagnose Lyme disease take days to weeks, which is unhelpful in acute clinical decision-making. Thus, some children with Lyme arthritis are treated empirically for septic arthritis undergoing unnecessary invasive procedures and hospital admission while on inappropriate antibiotic therapy. We retrospectively validated the Quidel Sofia Lyme Fluorescent Immunoassay, a rapid serologic assay that can detect IgG and/or IgM antibodies to Borrelia burgdorferi in 10 minutes, in residual serum samples collected from 51 children who had Lyme arthritis and 55 children with musculoskeletal presentations who were Lyme negative. The sensitivity and specificity of the Sofia IgG to identify cases of Lyme arthritis in children were 100% (95% confidence interval [CI] of 93.0%-100%) and 96.4% (95% CI: 87.5%-99.6%), respectively. The positive likelihood ratio (LR) was 27.5 (95% CI 7-107), and the negative LR was 0.00 (95% LR 0.00-0.15). We propose that the Sofia IgG, a rapid method for identifying Lyme arthritis, may be useful in differentiating Lyme arthritis from other forms of arthritis. Used in conjunction with readily available clinical and laboratory variables, it could help to rapidly identify children who are at low risk of septic arthritis in Lyme-endemic regions. IMPORTANCE: Lyme arthritis is a common manifestation of Lyme disease in children, with clinical features overlapping with other causes of acute and chronic joint pain/swelling in children. We have demonstrated that the Sofia IgG is a reliable test to rule in and rule out the diagnosis of Lyme arthritis in children with musculoskeletal presentations in a Lyme-endemic region. When used in conjunction with clinical and laboratory variables routinely considered when differentiating Lyme arthritis from other diagnoses, the Sofia IgG has the potential to fill an important gap in care, especially when acute decision-making is necessary. The Sofia IgG should be included in prospective research studies examining clinical prediction tools to identify children at low risk of septic arthritis.


Subject(s)
Antibodies, Bacterial , Arthritis, Infectious , Borrelia burgdorferi , Immunoglobulin G , Lyme Disease , Sensitivity and Specificity , Humans , Lyme Disease/diagnosis , Lyme Disease/blood , Child , Retrospective Studies , Male , Female , Antibodies, Bacterial/blood , Adolescent , Borrelia burgdorferi/immunology , Child, Preschool , Arthritis, Infectious/diagnosis , Arthritis, Infectious/microbiology , Diagnosis, Differential , Immunoglobulin G/blood , Immunoglobulin M/blood , Serologic Tests/methods
20.
Vaccine ; 42(7): 1768-1776, 2024 Mar 07.
Article in English | MEDLINE | ID: mdl-38368226

ABSTRACT

BACKGROUND: Two prefusion F protein-based vaccines, Arexvy and Abrysvo, have been approved by Health Canada for protecting older adults against respiratory syncytial virus (RSV)-associated lower respiratory tract disease. We estimated the health benefits and cost-effectiveness of these vaccines under a publicly funded single-dose vaccination program in Ontario that targets residents of long-term care homes (LTCHs). Additionally, we evaluated an extended program that broadens vaccination to include community-dwelling older adults. METHODS: A discrete-event simulation model was parameterised with the burden of RSV disease including outpatient care, hospitalisation, and death among adults aged 60 years or older in Ontario, Canada. Accounting for direct and indirect costs (in 2023 Canadian dollars) associated with RSV-related outcomes, we calculated the net monetary benefit using quality-adjusted life-year (QALY) gained, and determined the range of price-per-dose (PPD) for vaccination programs to be cost-effective from both healthcare and societal perspectives over two RSV seasons. The incremental cost-effectiveness ratio (ICER) was calculated to estimate the additional costs required to gain one QALY. RESULTS: Using a willingness-to-pay of $50,000 per QALY gained, we found that vaccinating 90% of residents in LTCHs with Arexvy would be cost-effective from a societal perspective for a PPD up to $163, producing a mean ICER value of $49,984 (95% CI: $47,539 to $52,704) per QALY gained with a two-year budget impact of $463,468 per 100,000 older adults. The reduction of hospitalizations was estimated at 7.0% compared to the no-vaccination scenario. Extending the program to include community-dwelling older adults with a 74% coverage akin to influenza vaccination, Arexvy remains cost-effective for a PPD up to $139, with a mean ICER value of $49,698 (95% CI: 48,022 to 51,388) per QALY gained and a two-year budget impact of $8.63 million. Compared to the no-vaccination scenario, the extended program resulted in a 57.3% reduction in RSV-related hospitalisations. CONCLUSIONS: Vaccinating residents of LTCHs against RSV disease would be cost-effective depending on PPD; extending the program to community-dwelling older adults would provide substantial health benefits, averting significant direct healthcare costs and productivity losses.


Subject(s)
Communicable Diseases , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus Vaccines , Respiratory Syncytial Virus, Human , Vaccines , Viral Vaccines , Humans , Aged , Cost-Benefit Analysis , Ontario , Respiratory Syncytial Virus Infections/prevention & control , Vaccination , Quality-Adjusted Life Years
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