Public Health Ontario Laboratory Research Articles

Geographic clustering of travel-acquired infections in Ontario, Canada, 2008-2020.

As the frequency of international travel increases, more individuals are at risk of travel-acquired infections (TAIs). In this ecological study of over 170,000 unique tests from Public Health Ontario's laboratory, we reviewed all laboratory-reported cases of malaria, dengue, chikungunya, and enteric fever in Ontario, Canada between 2008-2020 to identify high-resolution geographical clusters for potential targeted pre-travel prevention. Smoothed standardized incidence ratios (SIRs) and 95% posterior credible intervals (CIs) were estimated using a spatial Bayesian hierarchical model. High- and low-incidence areas were described using data from the 2016 Census based on the home forward sortation area of patients testing positive. A second model was used to estimate the association between drivetime to the nearest travel clinic and incidence of TAI within high-incidence areas. There were 6,114 microbiologically confirmed TAIs across Ontario over the study period. There was spatial clustering of TAIs (Moran's I = 0.59, p<0.0001). Compared to low-incidence areas, high-incidence areas had higher proportions of immigrants (p<0.0001), were lower income (p = 0.0027), had higher levels of university education (p<0.0001), and less knowledge of English/French languages (p<0.0001). In the high-incidence Greater Toronto Area (GTA), each minute increase in drive time to the closest travel clinic was associated with a 3% reduction in TAI incidence (95% CI 1-6%). While urban neighbourhoods in the GTA had the highest burden of TAIs, geographic proximity to a travel clinic in the GTA was not associated with an area-level incidence reduction in TAI. This suggests other barriers to seeking and adhering to pre-travel advice.

Estimating the test-adjusted incidence of Chlamydia trachomatis infections identified through Public Health Ontario Laboratories in Peel region, Ontario, 2010-2018: a population-based study.

Public health guidelines for chlamydia testing are not sex specific, but young females test at a disproportionally higher rate than males and other age groups. This study aims to describe testing trends across age and sex subgroups, then estimate a test-adjusted incidence of chlamydia in these subgroups to identify gaps in current testing practices. We used a population-based study to examine observed chlamydia rates by age and sex subgroups: 15-19 years, 20-29 years, 30-39 years and older than 40 years. The study included diagnostic test results recorded by Public Health Ontario Laboratories between Jan. 1, 2010, and Dec. 31, 2018, for individuals living in Peel region, Ontario. We then employed meta-regression models as a method of standardization to estimate the effect of sex and age on standardized morbidity ratio, testing ratio and test positivity, then calculate a test-adjusted incidence of chlamydia for each subgroup. Over the study period, infection, testing and test positivity varied across age and sex subgroups. Observed incidence and testing were highest in females aged 20-29 years, whereas males had the highest standardized test positivity across all age groups. After estimating test-adjusted incidence for each age-sex subgroup, males in the 15-19-year and 30-39-year age groups had an increase in incidence of 60.2% and 9.7%, respectively, compared with the observed incidence. We found that estimated test-adjusted incidence was higher than observed incidence in males aged 15-19 years and 30-39 years. This suggests that infections in males are likely being missed owing to differential testing, and this may be contributing to the persistent increase in reported cases in Canada. Public health programming that targets males, especially in high-risk settings and communities, and use of innovative partner notification methods could be critical to curbing overall rates of chlamydia.

Two Cases of Legionnaires’ disease following exposure to a hot tub at a private residence – Ontario, 2021

On September 10, 2021, the Haliburton, Kawartha, Pine Ridge District Health Unit in Ontario, Canada, received a case report of Legionella pneumophila serogroup 1 in a patient (case 1) hospitalized for pneumonia. A second case (case 2) within the same household was also identified. Case 1 was laboratory diagnosed by urine antigen testing, whereas case 2 was diagnosed by PCR and culture from a respiratory specimen collected from case 2, both at Public Health Ontario Laboratory, Ontario, Canada. Cases were linked by household and both cases were exposed via a newly purchased but previously used hot tub. Samples from the hot tub were culture positive when tested at PHO’s Laboratory. Given a respiratory culture isolate was available, together with an environmental isolate from the hot tub, sequence based typing was undertaken. Having both a clinical and an environmental culture isolate is essential for molecular investigations. The sequence type for the clinical isolate was the same as the environmental isolate, providing additional evidence that the hot tub was the source of infection for both cases.

Assessment of an enhanced COVID-19 case and contact management protocol in controlling a SARS-CoV-2 Alpha (B.1.1.7) variant outbreak on a construction site.

To control the spread of SARS-CoV-2 variants of concern (VOCs), Kingston, Frontenac, and Lennox & Addington (KFL&A) Public Health implemented a more stringent COVID-19 case and contact management (CCM) protocol than what was used across Ontario at the time. We describe epidemiological data and public health measures employed during one of the largest COVID-19 outbreaks in the KFL&A region at the time, caused by the SARS-CoV-2 Alpha (B.1.1.7) VOC, to assess this enhanced protocol. We obtained line lists of workers associated with the construction site outbreak, and subsequent cases and contacts from case investigators. Case testing, mutation status, and whole genome sequencing were conducted by Public Health Ontario Laboratories. From 409 high-risk contacts of the outbreak, 109 (27%) developed COVID-19. Three generations of spread were associated with the outbreak, affecting seven public health regions across three provinces. Using an enhanced approach to the CCM, KFL&A Public Health caught 15 cases that could have been missed by standard provincial protocols. Rapid initial spread within the construction site produced a relatively high attack rate among workers (26%) and their immediate contacts (34%). KFL&A Public Health's implementation of stringent CCM protocols and fast testing turn-around time effectively curbed the spread of the disease in subsequent generations - illustrated by the large reduction in attack rate (34%-14%) and cases (50-10) between the second and third generations. Lessons learned from this analysis may inform guidance on the CCM for future SARS-CoV-2 VOCs as well as other highly transmissible communicable diseases.

Increasing and More Commonly Refractory Mycobacterium avium Pulmonary Disease, Toronto, Ontario, Canada.

In mid-2014, Public Health Ontario Laboratories identified coincident increasing Mycobacterium avium isolation and falling M. xenopi isolation in the Toronto, Ontario, Canada, area. We performed a retrospective cohort of all patients in a Toronto clinic who began treatment for either M. avium or M. xenopi pulmonary disease during 2009–2012 (early period) or 2015–2018 (late period), studying their relative proportions and sputum culture conversion. We conducted a subgroup analysis among patients who lived in the Toronto-York region. The proportion of patients with M. avium was higher in the late period (138/146 [94.5%] vs. 82/106 [77.4%]; p<0.001). Among M. avium patients, conversion was lower in the late period (26.1% vs. 39.0%; p = 0.05). The increase in the proportion of patients with M. avium pulmonary disease and the reduction in the frequency of sputum culture conversion is unexplained but could suggest an increase in environmental M. avium exposure.

Assessment of population infection with SARS-CoV-2 in Ontario, Canada, March to June 2020.

BackgroundSerosurveys for SARS-CoV-2 aim to estimate the proportion of the population that has been infected.AimThis observational study assesses the seroprevalence of SARS-CoV-2 antibodies in Ontario, Canada during the first pandemic wave.MethodsUsing an orthogonal approach, we tested 8,902 residual specimens from the Public Health Ontario laboratory over three time periods during March–June 2020 and stratified results by age group, sex and region. We adjusted for antibody test sensitivity/specificity and compared with reported PCR-confirmed COVID-19 cases.ResultsAdjusted seroprevalence was 0.5% (95% confidence interval (CI): 0.1–1.5) from 27 March–30 April, 1.5% (95% CI: 0.7–2.2) from 26–31 May, and 1.1% (95% CI: 0.8–1.3) from 5–30 June 2020. Adjusted estimates were highest in individuals aged ≥ 60 years in March–April (1.3%; 95% CI: 0.2–4.6), in those aged 20–59 years in May (2.1%; 95% CI: 0.8–3.4) and in those aged ≥ 60 years in June (1.6%; 95% CI: 1.1–2.1). Regional seroprevalence varied, and was highest for Toronto in March–April (0.9%; 95% CI: 0.1–3.1), for Toronto in May (3.2%; 95% CI: 1.0–5.3) and for Toronto (1.5%; 95% CI: 0.9–2.1) and Central East in June (1.5%; 95% CI: 1.0–2.0). We estimate that COVID-19 cases detected by PCR in Ontario underestimated SARS-CoV-2 infections by a factor of 4.9.ConclusionsOur results indicate low population seroprevalence in Ontario, suggesting that public health measures were effective at limiting the spread of SARS-CoV-2 during the first pandemic wave.

737. Geographic Clustering of Travel-acquired Infections in Ontario, Canada, 2008-2020

BackgroundAs rates of international travel increase, more individuals are at risk of travel-acquired infections (TAIs). We aimed to review all microbiologically confirmed cases of malaria, dengue, chikungunya, and enteric fever (Salmonella enterica serovar Typhi/Paratyphi) in Ontario, Canada between 2008-2020 to identify high-resolution geographical clusters that could be targeted for pre-travel prevention.MethodsRetrospective cohort study of over 174,000 unique tests for the four above TAIs from Public Health Ontario Laboratories. Test-level data were processed to calculate annual case counts and crude population-standardized incidence ratios (SIRs) at the forward sortation area (FSA) level. Moran’s I statistic was used to test for global spatial autocorrelation. Smoothed SIRs and 95% posterior credible intervals (CIs) were estimated using a spatial Bayesian hierarchical model, which accounts for statistical instability and uncertainty in small-area incidence. Posterior CIs were used to identify high- and low-risk areas, which were described using sociodemographic data from the 2016 Census. Finally, a second model was used to estimate the association between drivetime to the nearest travel clinic and risk of TAI within high-risk areas.ResultsThere were 5962 cases of the four TAIs across Ontario over the study period. Smoothed FSA-level SIRs are shown in Figure 1a, with an inset for the Greater Toronto Area (GTA) in 1b. There was spatial clustering of TAIs (Moran’s I=0.61, p< 2.2e-16). Identified high- and low-risk areas are shown in panels c and d. Compared to low-risk areas, high-risk areas were significantly more likely to have higher proportions of immigrants (p< 0.0001), lower household after-tax income (p=0.04), more university education (p< 0.0001), and were less knowledgeable of English/French (p< 0.0001). In the high-risk GTA, each minute increase in drivetime to the closest travel clinic was associated with a 4% reduction in TAI risk (95% CI 2 - 6%). Bayesian hierarchical model (BHM) smoothed standardized incidence ratios (SIRs) for travel-acquired infections (TAIs) and estimated risk levels (a and c) with insets for the Greater Toronto Area (b and d). High-risk areas are defined as those with smoothed SIR 95% CIs greater than 2, and low-risk areas with smoothed SIR 95% CIs less than 0.25.ConclusionUrban neighbourhoods in the GTA had elevated risks of becoming ill with TAIs. However, geographic proximity to a travel clinic was not associated with an area-level risk reduction in TAI, suggesting other barriers to seeking and adhering to pre-travel advice.Disclosures Isaac Bogoch, MD, MSc, BlueDot (Consultant)National Hockey League Players' Association (Consultant) Andrea Boggild, MSc MD DTMH FRCPC, Nothing to disclose Shaun Morris, MD, MPH, DTM&H, FRCPC, FAAP, GSK (Speaker's Bureau)Pfizer (Advisor or Review Panel member)Pfizer (Grant/Research Support)

Antimicrobial susceptibility profiles of invasive isolates of anaerobic bacteria from a large Canadian reference laboratory: 2012–2019

Anaerobic bacteria can cause severe and life threatening infections. Susceptibility data are relatively limited on anaerobic organisms despite the clinical importance in guiding empiric treatment of infections. To determine antimicrobial susceptibility profiles of clinically significant anaerobic bacteria, isolates obtained from sterile sites submitted to Public Health Ontario Laboratory (2012–2019) were included in this study (N = 5712). Cefoxitin, clindamycin, metronidazole, meropenem, penicillin and piperacillin-tazobactam were tested using the gradient strip method with MICs interpreted based on Clinical and Laboratory Standards Institute guidelines. Bacteroides spp. (N = 958; 16.7%), Clostridium spp. (N = 798; 14.0%), Cutibacterium spp. (N =659; 11.5%) and Actinomyces spp. (N = 551; 7.0%) were the most commonly isolated genera. Bacteroides fragilis isolates were susceptible to cefoxitin (88.4%), clindamycin (68.4%), metronidazole (96.0%), meropenem (99.0%) and piperacillin-tazobactam (98.4%). Other Bacteroides spp. showed reduced susceptibility to several antimicrobials. Clostridium spp. isolates were susceptible to penicillin (69.7%), clindamycin (69.7%) and cefoxitin (76.3%); C. perfringens and C. ramosum showed distinct susceptibility profiles. Susceptibility rates among anaerobes remained relatively unchanged over 8 years with a few exceptions: C. perfringens susceptibility to clindamycin decreased from 91.3% to 60% (p = 0.03); Clostridium spp. susceptibility to penicillin similarly decreased from 82.1% to 65.9% (p = 0.03); Eggerthella spp. susceptibility to piperacillin-tazobactam decreased from 100% to 24.3% (p < 0.001); B. fragilis group susceptibility to cefoxitin decreased from 70.4% to 48.2% (p = 0.05); and Parabacteroides spp. susceptibility to piperacillin-tazobactam decreased from 100% to 25% (p = 0.01). Our findings underscore the need for ongoing surveillance and periodic monitoring of antimicrobial resistance in order to guide empiric therapy.

Investigation of a severe SARS-CoV-2 outbreak in a long-term care home early in the pandemic.

BACKGROUND:The implementation of outbreak management measures has decreased the frequency and severity of SARS-CoV-2 outbreaks in Ontario long-term care homes. We describe the epidemiological and laboratory data from one of the first such outbreaks in Ontario to assess factors associated with its severity, and the impact of progressive interventions for infection control over the course of the outbreak.METHODS:We obtained line list and outbreak data from the public health unit to describe resident and staff cases, severity and distribution of cases over time and within the outbreak facility. Where available, we obtained data on laboratory specimens from the Public Health Ontario Laboratory and performed whole genome sequencing and phylogenetic analysis of viral specimens from the outbreak.RESULTS:Among 65 residents of the long-term care home, 61 (94%) contracted SARS-CoV-2, with a case fatality rate of 45% (28/61). Among 67 initial staff, 34 (51%) contracted the virus and none died. When the outbreak was declared, 12 staff, 2 visitors and 9 residents had symptoms. Resident cases were located in 3 of 4 areas of the home. Phylogenetic analysis showed tight clustering of cases, with only 1 additional strain of genetically distinct SARS-CoV-2 identified from a staff case in the third week of the outbreak. No cases were identified among 26 new staff brought into the home after full outbreak measures were implemented.INTERPRETATION:Rapid and undetected viral spread in a long-term care home led to high rates of infection among residents and staff. Progressive implementation of outbreak measures after the peak of cases prevented subsequent staff cases and are now part of long-term care outbreak policy in Ontario.

COVID-19 outbreak in a personal service setting in Kingston, Ontario, 2020.

During the coronavirus disease 2019 (COVID-19) pandemic, Ontario created a three-phase reopening framework for the economy. Outbreaks were expected at each phase. One week after Phase Two of reopening in the provincial public health administration region of Kingston, Frontenac, Lennox and Addington (KFL&A), a positive case was reported after three weeks of zero new COVID-19 cases. The objective of this report is to describe this COVID-19 outbreak, linked to a personal service setting (PSS), and the public health response to contain the outbreak. The outbreak investigation included all COVID-19 cases in KFL&A between June 20, 2020 and July 3, 2020. Public health inspectors and nurses were rapidly deployed to inspect the PSS. A multimodal approach to high-volume testing involved fixed assessment centres, drive-through testing capacity and targeted testing at the outbreak site. Testing was conducted through a real-time polymerase chain reaction assay at the local Public Health Ontario laboratory. Thirty-seven cases were associated with the outbreak: 38% through direct PSS exposure; 32% through household contact; and 30% through social and workplace contact. A superspreading event contributed to 38% of total cases. The majority of cases were in the low to mid-quintiles when analyzed for material deprivation. Testing rates increased four-fold compared to the prior baseline weeks in response to media attention and public health messaging, resulting in a low percent positivity. The interplay of aggressive accessible testing, quick lab turnaround time, contact tracing within 24 hours of positive laboratory results as per provincial standards, frequent public communication, rapid inspections, mandatory self-isolation and face coverings were measures successful in halting the outbreak. Inspections or self-audits should be required at all PSSs prior to reopening and outbreak management must work with PSSs to reduce the possibility of superspreading events.

Prevalence of Co-Infections with Respiratory Viruses in Individuals Investigated for SARS-CoV-2 in Ontario, Canada.

Background: Co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with respiratory viruses, bacteria and fungi have been reported to cause a wide range of illness. Objectives: We assess the prevalence of co-infection of SARS-CoV-2 with seasonal respiratory viruses, document the respiratory viruses detected among individuals tested for SARS-CoV-2, and describe characteristics of individuals with respiratory virus co-infection detected. Methods: Specimens included in this study were submitted as part of routine clinical testing to Public Health Ontario Laboratory from individuals requiring testing for SARS-CoV-2 and/or seasonal respiratory viruses. Results: Co-infection was detected in a smaller proportion (2.5%) of individuals with laboratory confirmed SARS-CoV-2 than those with seasonal respiratory viruses (4.3%); this difference was not significant. Individuals with any respiratory virus co-infection were more likely to be younger than 65 years of age and male than those with single infection. Those with SARS-CoV-2 co-infection manifested mostly mild respiratory symptoms. Conclusions: Findings of this study may not support routine testing for seasonal respiratory viruses among all individuals tested for SARS-CoV-2, as they were rare during the study period nor associated with severe disease. However, testing for seasonal respiratory viruses should be performed in severely ill individuals, in which detection of other viruses may assist with patient management.

Clinical and Genetic Characteristics of Extended-Spectrum Beta-Lactamase–Producing Enterobacteriaceae Among Canadian Children

Background: Infections with extended-spectrum β-lactamase–producing Enterobacteriaceae (ESBL-E) in nonoutbreak settings have not demonstrated the presence of dominant strains. Our objective was to determine the incidence, clinical characteristics, and genetic characteristics of ESBL-E infections among a group of Canadian children. Methods: From 2012 through 2017, patients aged ≤18 years with first-episode ESBL-E infections who presented at a pediatric center were reviewed. All clinical isolates were phenotypically identified in the laboratory as ESBL-producers. Demographic and clinical data were collected, including comorbid conditions, presence of devices, and previous antibacterial exposure. Community-associated infection was defined as a positive culture from a sterile site within the first 48 hours of hospital admission and no healthcare exposure during the preceding year. Isolates were sent to the Public Health Ontario Laboratory for whole-genome sequencing. Multilocus sequence typing was used to determine clonal relationship. Results: During the study period, 102 patients were identified with first-episode ESBL-E infection, and the proportion of ESBL-E isolates among all clinical isolates of E. coli and Klebsiella spp increased from 0.6% to 2.6% between 2012 and 2017, respectively (P = .001). The median age was 1 year (interquartile range, 0.8–5 years). Women comprised 66% of cases. No comorbid conditions were noted among 58 patients (57%), and 24% had previous antibiotic exposure, most frequently a cephalosporin (16%). ESBL-E was most frequently isolated in the urine (91%) and least frequently in the blood (2.2%) and was predominantly Escherichia coli (90%). Infection was most frequently diagnosed in the outpatient setting (61%); there were 11 healthcare-associated infections. Whole-genome sequencing of ESBL-E isolates revealed predominance of blaCTX-M-15 (63 isolates, 62%) and blaCTX-M-27 (16%) genes, and sequence type (ST) 131 (41%). Mutations conferring fluoroquinolone nonsusceptibility were noted among 62 isolates (61%), most frequently associated with ST131 (38 of 62 isolates, 61%) and among all 5 isolates with ST1193, an emerging multidrug-resistant E. coli clone. In addition, 15 patients had recurrence of ESBL-E infection at median of 113 days (IQR, 26–208); blaCTX-M-27 was found in 33% of recurrent infections compared to 12% of primary infections (P = 0.045). Conclusions: This study is the first in Canada to provide whole-genome sequencing data regarding ESBL-E in a pediatric population. The gene blaCTX-M-15 and ST131 clone were predominant. More than 60% of infections were community associated and demonstrated cross resistance to fluoroquinolones. With 76% of infections in antibiotic-naïve children, ESBL-E is a public health concern, and a One Health approach is critical to understanding the epidemiology and curbing the spread of multidrug-resistant Enterobacteriaceae.Funding: NoneDisclosures: None

Examining the association between stress and antiretroviral therapy adherence among women living with HIV in Toronto, Ontario

Background We aimed to identify the association between stress and antiretroviral therapy (ART) adherence among women in HIV care in Toronto, Ontario participating in the Ontario HIV Treatment Network Cohort Study (OCS) between 2007 and 2012. Materials and methods We conducted cross-sectional analyses with women on ART completing the AIDS Clinical Trial Group (ACTG) Adherence Questionnaire. Data closest to, or at the last completed interview, were collected from medical charts, through record linkage with Public Health Ontario Laboratories, and from a standardized self-reported questionnaire comprised of socio-demographic and psycho-socio-behavioral measures (Center for Epidemiologic Studies Depression Scale (CES-D), Alcohol Use Disorders Identification Test (AUDIT)), and stress measures (National Population Health Survey). Logistic regression was used to quantify associations with optimal adherence (≥95% adherence defined as missing ≤ one dose of ART in the past 4 weeks). Results Among 307 women, 65.5% had optimal adherence. Women with suboptimal compared to optimal adherence had higher median total stress scores (6.0 [interquartile range (IQR): 3.0–8.1] vs. 4.1 [IQR: 2.0–7.1], p = 0.001), CES-D scores (16 [IQR: 6–28] vs. 12 [IQR: 3–22], p = 0.008) and reports of hazardous and harmful alcohol use (31.1% vs. 17.9%, p = 0.008). In our multivariable model, we found an increased likelihood of optimal adherence with the absence of hazardous and harmful alcohol use (Adjusted Odds Ratio (AOR)=2.20, 95% confidence interval (CI): 1.12–4.32) and a decreased likelihood of optimal adherence with more self-reported stress (AOR = 0.56, 95% CI: 0.33–0.94). Conclusions Interventions supporting optimal ART adherence should address stress and include strategies to reduce or eliminate hazardous and harmful alcohol use for women living with HIV.

Mycobacteriosis in a Zoo Population of Chinese Gliding Frogs (Rhacophorus dennysi) Due to Mycobacterium marinum

Mycobacteriosis was implicated in the deaths of eight Chinese gliding frogs (Rhacophorus dennysi) in a zoo population over a 3 yr period. Clinical signs included nonhealing skin lesions, cloacal prolapse, hind limb weakness, weight loss, and sudden death. Abnormalities on postmortem were proliferative or ulcerative skin lesions in four of eight, pneumonia in three of eight, and gall bladder empyema in two of eight cases. All eight clinical cases had multisystemic granulomas containing acid-fast bacilli. Tissues most commonly affected were lung (seven of eight), liver (six of eight), kidney (six of eight), spleen (five of eight), and heart (five of eight). The remaining eight clinically normal frogs in the population were euthanized: eight of eight had granulomatous lesions, with acid-fast bacilli in three of eight cases. A mycobacterial species was cultured from four of the clinical cases by the Public Health Ontario Laboratory and was initially misidentified as Mycobacterium tuberculosis complex by a commercial line-probe assay (GenoType Mycobacterium CM, Hain Lifesciences, Nehren, Germany). Further diagnostic testing using 16S rRNA gene sequencing ultimately identified the mycobacterial species as Mycobacterium marinum. The correct identification of mycobacterial species is essential in epidemiological investigations at zoological facilities, and in assessing health risks to staff and to other animals in the zoo population.

Infection prevention and control lapse involving medical equipment reprocessing at a family medicine clinic in Ottawa, Ontario, 2018.

In April 2018, Ottawa Public Health identified a large-scale infection prevention and control (IPAC) lapse spanning 15 years related to inadequate reprocessing of reusable critical medical equipment used in a family medicine clinic. To describe the public health response to, and estimate the risk of hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV) transmission from, this IPAC lapse. Patients who underwent a procedure of concern (during which reusable equipment may have been used) at this clinic were identified using Ontario Health Insurance Plan data and individually notified. Testing for HBV, HCV and HIV at the Public Health Ontario Laboratory was recommended, and the odds of infection were estimated. Of 4,495 patients possibly exposed to improperly reprocessed equipment, 1,496 (33.3%) underwent testing within six months of notification. The prevalence of HBV, HCV and HIV infection in this group was lower than in the general Canadian population. Among patients first diagnosed with HBV after a procedure of concern, the odds of HBV transmission were not increased when the procedure occurred within seven or 28 days of another patient with a positive HBV test result (OR7 days, age-adjusted=0.59, 95% CI: 0.14-2.51; OR28 days, age-adjusted=1.35, 95% CI: 0.62-2.93). The odds of HCV and HIV transmission could not be estimated because no patient was diagnosed with HCV or HIV after having a procedure of concern within 28 days of another patient with a positive HCV or HIV test result. We found no evidence of HBV, HCV or HIV transmission associated with this IPAC lapse. However, transmission cannot be ruled out conclusively because only a third of possibly exposed patients underwent testing.

The evolving nature of Bordetella pertussis in Ontario, Canada, 2009-2017: strains with shifting genotypes and pertactin deficiency.

This study examined the evolving nature of Bordetella pertussis in Ontario, Canada, by characterizing isolates for their genotypes and expression of pertactin (PRN). From 2009 to 2017, 413 B. pertussis were cultured from pertussis cases at the Public Health Ontario Laboratory. Their genotypes were determined by partial gene sequence analysis of their virulence and (or) vaccine antigens: filamentous haemagglutinin, PRN, fimbriae 3, and pertussis toxin, including the promoter region. Expression of PRN was measured by Western immunoblot. Two predominant genotypes, ST-1 and ST-2, were found throughout the study and were responsible for 47.5% and 46.3% of all case isolates, respectively. The prevalence of ST-1 appeared to fluctuate from 80.3% in 2009 to 20.0% in 2014 and 58.5% in 2017, while the prevalence of ST-2 changed from 18.4% in 2009 to 80.0% in 2014 and 26.2% in 2017. A PRN-deficient strain was first noted in 2011 (16.7%), and its prevalence increased to 70.8% in 2016 but decreased to 46.2% in 2017. More ST-2 (46.6%) than ST-1 (16.8%) strains were associated with PRN deficiency. Newer ST-21 and ST-22 found in 2015-2017 were uniformly PRN deficient. The impact of the evolving nature of B. pertussis on disease epidemiology requires further longitudinal studies.

Application of whole genome sequencing to query a potential outbreak of Elizabethkingia anophelis in Ontario, Canada.

Bioinformatic analysis of whole genome sequence (WGS) data is emerging as a tool to provide powerful insights for clinical microbiology. We used WGS data to investigate the genetic diversity of clinical isolates of the bacterial pathogen Elizabethkingia anophelis to query the existence of a single-strain outbreak in Ontario, Canada. The Public Health Ontario Laboratory (PHOL) provides reference identification of clinical isolates of bacteria for Ontario and prior to 2016 had not identified E. anophelis . In the wake of the Wisconsin outbreak of 2015–2016 for which a source was never elucidated, the identification of E. anophelis from clinical specimens from five Ontario patients gave reason to question the presence of an outbreak. Genomic comparisons based on core genome multi-locus sequence typing conclusively refuted the existence of an outbreak, since the 5 Ontario isolates were genetically dissimilar, representing at least 3 distinct sub-lineages scattered among a set of 39 previously characterized isolates. Further interrogation of the genomic data revealed multiple antimicrobial resistance genes. Retrospective reidentification via rpoB sequence analysis of 22 clinical isolates of Elizabethkingia spp. collected by PHOL from 2010 to 2018 demonstrated that E. anophelis was isolated from clinical specimens as early as 2010. The uptick in E. anophelis in Ontario was not due to an outbreak or increased incidence of the pathogen, but rather enhanced laboratory identification techniques and improved sequence databases. This study demonstrates the usefulness of WGS analysis as a public health tool to quickly rule out the existence of clonally related case clusters of bacterial pathogens indicative of single-strain outbreaks.

Intercurrent flaviviral viremia and Plasmodium ovale infection in ill returned travelers to Ontario

Purpose: Similar epidemiology and clinical presentations of arboviral infections and malaria along with the typically sequential approach to diagnostic testing, with malaria excluded urgently in febrile returned travelers, may mask the true epidemiology of such dual infections. Flaviviruses have been reported to trigger relapsing forms of malaria, including Plasmodium ovale, long after primary malarial infection, and this may delay the diagnosis of malaria. We aim to understand the incidence of intercurrent flaviviral infection in cases of confirmed Plasmodium ovale infection, where the flavivirus may have triggered relapse. Methods & Materials: DNA and RNA from biobanked isolates of P. ovale detected in whole blood at the Public Health Ontario Laboratory between 2006 and 2018 will be extracted and screened for intercurrent flaviviral infections using previously validated real-time PCR (qPCR) assays targeting multiple flaviviruses (pan-FLAV) and specifically dengue virus types 1–4 (DEN1, DEN2, DEN3, DEN4). Results: One-hundred fifteen unique isolates of P. ovale were identified over the reporting period, of which 62 had sufficient specimen for further molecular analysis. Among analyzed cases, over half occurred in males (36/62 [58%]), over a third occurred in females (23/36 [37%]), and 5% (3/62) had unassigned sex. Median age of P. ovale cases was 28.8 years (range 22 mos - 72 years; IQR 18.8–40.1 years). Median parasitemia was < 0.01% (range < 0.01% - 0.8%). Thirty (48%) P. ovale cases had documented travel history exclusively to Africa, with Nigeria as the most common source country (22/54 [40.1%]). Pan-FLAV assay yielded a 1.6% (1/62) positivity rate. DEN1-4 assay results are pending. Conclusion: P. ovale infections are most commonly imported to Ontario from West Africa, and Nigeria, specifically. Intercurrent flaviviral viremia was noted in at least 1.6%, which may suggest that primary flaviviral infection triggered a relapse of P. ovale. Alternatively, such co-occurrence may suggest primary infection with both organisms known to cause fever in returning travelers. Consideration of flaviviral co-infection should be given to the P. ovale patient with deep thrombocytopenia, lymphopenia, and high-yield arboviral symptomatology such as rash and retro-orbital headache. The influence of flaviviruses on the clinical course of P. ovale should be examined prospectively.

Occurrence and distribution of Ambylomma americanum as determined by passive surveillance in Ontario, Canada (1999–2016)

The lone star tick, Amblyomma americanum, is spreading northward from its historical stronghold in the southeastern United States. As a vector and biting pest, public and veterinary health officials must remain vigilant of the lone star tick’s expanding range. We use ticks submitted to Public Health Ontario Laboratory (1999–2016) to describe the spatial and temporal dynamics of A. americanum in Ontario, Canada, as well as submitter demographics. We identified 847 A. americanum submissions during the surveillance period, with 773 (91.3%) non-travel-related and 74 (8.7%) travel-related submissions. Annual A. americanum submissions increased over the surveillance period. Approximately 91% of non-travel-related submissions were adult ticks and 9% were nymphs. The highest submission rates were from individuals living in the Eastern and South West regions of the province. Adult specimens were primarily submitted from May through July and nymphs from March through September. Higher numbers of submissions were from young children (<10 years) and older adults (55–74 years), with equal proportions of male and female submitters. The majority of travel-related submissions were from travellers returning from the southeastern United States (i.e., Florida, North Carolina, South Carolina, Tennessee, Texas). Amblyomma americanum distribution is scattered in Ontario and submissions are likely the consequence of ongoing detection of adventive specimens. Further tick dragging is required to confirm the presence of established lone star tick populations in the province. Given the relatively rapid expansion of blacklegged ticks, Ixodes scapularis, populations in Ontario, we expect climate change to facilitate the range of expansion of A. americanum into the province. We propose an algorithm for identifying A. americanum-risk areas, which will aid public and veterinary health officials when assessing the risks posed by lone star ticks.

Sputum smear microscopy predicting mycobacterial culture in Ontario: A population-based laboratory report

RATIONALE: Tuberculosis (TB) and nontuberculous mycobacterial (NTM) pulmonary disease may present similarly but must be swiftly distinguished because of public health implications. The first diagnostic test usually available for suspected pulmonary mycobacterial disease is smear microscopy for acid-fast bacilli (AFB).OBJECTIVES: To measure the diagnostic utility of sputum AFB in Ontario.METHODS: All patients’ first AFB smears submitted to Public Health Ontario Laboratories during 2012–2014 were compared against final cultures. Diagnostic test characteristics were calculated for AFB smears in predicting TB and NTM separately.MEASUREMENTS AND MAIN RESULTS: Among 30 136 patients, AFB smears and cultures were positive in 4.2% (1279) and 17.4% (5233) respectively, comprising TB in 800 (2.7%, AFB-positive 489 [61.1%]) and NTM in 4433 (14.7%, AFB-positive 652 [14.7%]). Test characteristics for TB were: specificity 97.3%, negative predictive value 98.9%, sensitivity 61.1%, and positive predictive value 38.2%. Performance improved somewhat in males: specificity 97.4%, negative predictive value 98.8%, sensitivity 60.1%, positive predictive value 42.0%, and more so in people <60 years old: specificity 98.3%, negative predictive value 98.5%, sensitivity 60.9%, positive predictive value 56.8%. Test characteristics for NTM were: specificity 97.6%, negative predictive value 86.9%, sensitivity 14.7%, positive predictive value 51.0% in the entire population.CONCLUSIONS: Sputum AFB performed poorly in predicting TB because of the large proportion of AFB-positives caused by NTM (51.0%) and the relatively small proportion of AFB-positive TB cases (61.1%). The predictive ability for NTM was also poor. Regardless of age and sex, AFB remained an inadequate predictor of TB and NTM in Ontario.