National Microbiology Laboratory Research Articles

Whole Genome Sequencing for the Identification of a Streptococcus agalactiae Outbreak in Neonatal Intensive Care Unit

Background: While Streptococcus agalactiae (Group B Streptococcus [GBS]) infections in infants usually result from maternal transmission, healthcare-associated cases, particularly in the neonatal intensive care unit (NICU), can occur. Whole genome sequencing (WGS) can aid in investigating GBS outbreaks among infants in hospital settings. The aim of the study is to describe the investigation of GBS infections in NICU using WGS. Methods: Infection prevention and control (IPAC) at our hospital monitors the occurrence of late-onset GBS disease (LOD) in our 57-bed NICU, which consists of all private rooms. The occurrence of 2 cases of LOD within 2 weeks triggered an investigation, including WGS of the two isolates and isolates causing invasive GBS during the last 6 months in the unit. GBS isolates underwent WGS using Illumina at Canada’s National Microbiology Laboratory. All affected patients underwent chart-review. Outbreak description and investigation: In August 2023, two NICU neonates (patients 2,3) experienced LOD two weeks apart, one with bacteremic meningitis and the other with two bacteremic episodes three weeks apart. While WGS was pending two additional cases of late-onset GBS bacteremia (patients 4,5) occurred. Isolates from Pts 2,3 and 5 were indistinguishable from each other and from an isolate from an infant admitted to the NICU with early onset bacteremia on July 27, 2023 (day 1 of life) (patient 1). Weekly point prevalence for throat and rectal colonization over 3 weeks identified five infants colonized with unrelated strains. An additional long-stay infant (patient 6) developed GBS conjunctivitis due to a strain indistinguishable from (patient 4) by pulse field gel electrophoresis, WGS for the second cluster is pending. IPAC interventions: Lapses in IPAC practices were observed, with no commonalities among cases other than similar geographic location within the unit. We hypothesized transmission was due to horizontal transmission between babies due to these lapses. Basic IPAC measures, including hand hygiene and environmental cleaning, were reinforced; Additional Precautions were not used due to private rooms’ unit structure. No environmental samples were taken due to lack of an obvious environmental point or common source. Point prevalence monitoring persisted until no new cases related to the outbreak strains were further identified in three consecutive weekly point prevalence. Conclusions: Increased awareness of healthcare-associated transmission is crucial in NICU as LOD GBS emerges. WGS plays a key role in identifying transmission. Detecting a multi-strain outbreak can appropriately redirect investigations. Legend: Figure 1: Timeline of stay at NICU and infection timing for patients 1-6

Healthcare-associated infections and antimicrobial resistance in Canadian acute care hospitals, 2018-2022.

Healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) continue to contribute to excess morbidity and mortality among Canadians. This report describes epidemiologic and laboratory characteristics and trends of HAIs and AMR from 2018 to 2022 (Candida auris, 2012-2022) using surveillance and laboratory data submitted by hospitals to the Canadian Nosocomial Infection Surveillance Program (CNISP) and by provincial and territorial laboratories to the National Microbiology Laboratory. Data collected from 88 Canadian sentinel acute care hospitals between January 1, 2018, and December 31, 2022, for Clostridioides difficile infections (CDIs), carbapenemase-producing Enterobacterales (CPE) infections, methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSIs) and vancomycin-resistant Enterococcus (VRE) BSIs. Candida auris (C. auris) surveillance was initiated in 2019 by CNISP and in 2017 (retrospectively to 2012) by the National Microbiology Laboratory. Trend analysis for case counts, rates, outcomes, molecular characterization and AMR profiles are presented. From 2018 to 2022, decreased rates per 10,000 patient days were observed for CDIs (7% decrease; 5.42-5.02) and MRSA BSIs (2.9% decrease; 1.04-1.01). Infection rates for VRE BSIs increased by 5.9% (0.34-0.36). Infection rates for CPE remained low but increased by 133% (0.06-0.14). Forty-three C. auris isolates were identified in Canada from 2012 to 2022, with the majority in Western and Central Canada (98%). From 2018 to 2022, the incidence of MRSA BSIs and CDIs decreased and VRE BSI and CPE infections increased in the Canadian acute care hospitals participating in a national sentinel network (CNISP). Few C. auris isolates were identified from 2012 to 2022. Reporting standardized surveillance data to inform the application of infection prevention and control practices in acute care hospitals is critical to help decrease the burden of HAIs and AMR in Canada.

Invasive pneumococcal disease surveillance in Canada, 2021-2022.

Invasive pneumococcal disease (IPD, Streptococcus pneumoniae) has been a nationally notifiable disease in Canada since 2000. The use of conjugate vaccines has caused a shift in the distribution of serotypes over time. This report is a summary of the demographics, serotypes and antimicrobial resistance of IPD isolates collected in Canada in 2021 and 2022. The National Microbiology Laboratory (NML) of the Public Health Agency of Canada in Winnipeg, Manitoba collaborates with provincial and territorial public health laboratories to conduct national surveillance of IPD. There were 1,999 isolates reported in 2021 and 3,775 isolates in 2022. Serotype was determined by the Quellung reaction or whole-genome sequencing (WGS). Antimicrobial susceptibilities were determined by WGS methods, broth microdilution, or data shared by collaborators in the Canadian Antimicrobial Resistance Alliance program at the University of Manitoba. Population-based IPD incidence rates were obtained through the Canadian Notifiable Disease Surveillance System. The incidence of IPD in Canada was 5.62 cases per 100,000 population in 2021, decreasing from the peak of 10.86 cases per 100,000 population in 2018. Serotypes with increasing trends (p<0.05) between 2018 and 2022 included: 4 (6.1%-12.4%), 9V (1.0%-5.1%) and 12F (4.8%-5.4%). The overall prevalence of PCV13 serotypes increased over the same period (31.2%-41.5%, p<0.05) while the prevalence of non-vaccine types decreased significantly (27.3%-21.5%, p<0.0001). The highest rates of antimicrobial resistance in 2021 and 2022 were seen with clarithromycin (21%, 2021; 24%, 2022) and erythromycin (22%, 2021; 24%, 2022). Multidrug-resistant IPD continued to increase from 2018 to 2022 (6.7%-12.6%, p<0.05). The number of cases of IPD continued to decrease in 2021 in comparison to previous years, however, 2022 saw a return to pre-COVID-19 levels. Disease due to PCV13 serotypes 3, 4, 9V and 19F, as well as non-PCV13 serotypes 12F and 20, is increasing in prevalence. Surveillance of IPD to monitor changing serotype distribution and antimicrobial resistance is essential.

Invasive group A streptococcal disease surveillance in Canada, 2021-2022.

Invasive group A streptococcal (iGAS, Streptococcus pyogenes) disease has been a nationally notifiable disease in Canada since 2000. This report summarizes the demographics, emm types, and antimicrobial resistance of iGAS isolates collected in Canada in 2021 and 2022. The Public Health Agency of Canada's National Microbiology Laboratory collaborates with provincial and territorial public health laboratories to conduct national surveillance of invasive S. pyogenes. Emm typing was performed using the Centers for Disease Control and Prevention emm sequencing protocol or extracted from whole-genome sequencing data. Antimicrobial susceptibilities were determined using Kirby-Bauer disk diffusion according to Clinical and Laboratory Standards Institute guidelines or predicted from whole-genome sequencing data based on the presence of resistance determinants. Overall, the incidence of iGAS disease in Canada was 5.56 cases per 100,000 population in 2021, decreasing from the peak of 8.6 cases per 100,000 population in 2018. A total of 2,630 iGAS isolates were collected during 2022, representing an increase from 2021 (n=2,179). In particular, there was a large increase in isolates collected from October to December 2022. The most predominant emm type overall in 2021 and 2022 was emm49, at 21.5% (n=468) and 16.9% (n=444), respectively, representing a significant increase in prevalence since 2018 (p<0.0001). The former most prevalent type, emm1, increased from 0.5% (n=10) in 2021 to 4.8% (n=125) in 2022; similarly, emm12 increased from 1.0% (n=22) in 2021 to 5.8% (n=151) in 2022. These two types together accounted for almost 25% of isolates collected in late 2022 (October to December). Antimicrobial resistance rates in 2021 and 2022 included: 14.9%/14.1% erythromycin resistance, 4.8%/3.0% clindamycin resistance, and <1% chloramphenicol resistance. The increase of iGAS isolates collected in Canada is an important public health concern. Continued surveillance of iGAS is critical to monitor expanding emm types and antimicrobial resistance patterns.

Antimicrobial susceptibilities of Neisseria gonorrhoeae in Canada, 2021.

In Canada, gonorrhea is the second most prevalent bacterial sexually transmitted infection. The Gonococcal Antimicrobial Surveillance Programme (GASP - Canada), a passive surveillance system monitoring antimicrobial resistance in Neisseria gonorrhoeae in Canada since 1985, is the source for this summary of demographics, antimicrobial resistance and N. gonorrhoeae multi-antigen sequence typing (NG-MAST) of gonococcal isolates collected in Canada in 2021. Provincial and territorial public health laboratories submitted N. gonorrhoeae cultures and data to the National Microbiology Laboratory in Winnipeg as part of the surveillance system. The antimicrobial resistance and molecular type of each isolate received were determined. In total, 3,439 N. gonorrhoeae cultures were received from laboratories across Canada in 2021, a 9.9% increase since 2020 (n=3,130). Decreased susceptibility to cefixime increased significantly (p<0.001) in 2021 (1.5%) compared to 2017 (0.6%). No significant change in decreased susceptibility to ceftriaxone was detected between 2017 and 2021 (0.6%) (p>0.001); however, one ceftriaxone-resistant isolate was identified. Azithromycin resistance decreased significantly (p<0.001) in 2021 (7.6%) compared to 2017 (11.7%); however, there was a significant increase (p<0.001) in the proportion of cultures with an azithromycin minimum inhibitory concentration of at least 1 mg/L (2017=22.2% to 2021=28.1%). In 2021, NG-MAST-19875 (15.3%) was the most prevalent sequence type in Canada; 20.3% of isolates with this sequence type were resistant to azithromycin. The spread of antimicrobial-resistant gonorrhea is a significant public health concern. The continued regional and national surveillance of antimicrobial resistance in N. gonorrhoeae is essential in ensuring effective treatment therapies are recommended.

C9 (Clinical Case) Monkeypox Virus Infection in a 2-Month-Old Infant

Abstract Introduction/Background The 2022 Monkeypox virus outbreak shed attention on an illness that is rare in non-endemic countries. Children are at risk of severe disease based on case series from previous outbreaks. Tecovirimat may be considered as a therapy in young children. Its efficacy and safety profile, however, have never been formally studied. This case report presents the first laboratory-confirmed case of monkeypox virus infection in a Canadian infant and its management. Case Description A 2-month-old infant presented to an emergency department with a vesiculopustular skin rash. A week before, parents noticed an eruptive cluster of 3 fluid-filled vesicles on the infant’s forehead. In the next days, vesiculopustular lesions appeared on his body. One spike of temperature was reported with no other sign of illness. On physical examination, a dozen umbilicated well-circumscribed vesico-pustules were observed with minimal skin inflammation. They ranged from 2 to 5 mm in size and were scattered over the face, trunk and limbs including palms and soles. In addition, 3 confluent crusted umbilicated lesions were present on the forehead. Discussion Differential diagnosis included varicella zoster virus, herpes simplex virus, and enteroviral infections. Empiric intravenous acyclovir was initiated pending specimen analysis. Bacterial culture and viral PCRs were negative on CSF and skin specimens. Due to transmission of monkeypox in the local adult population, orthopoxvirus was tested by PCR. The result was positive on a skin specimen and was later confirmed by the National Microbiology Laboratory of Canada. Because of the patient’s age and ongoing new lesions, tecovirimat was initiated. After 24 hours, new lesions stopped appearing and regression and crusting of active lesions were noted. Treatment was continued for 14 days without adverse events. Although parents denied similar symptoms, an epidemiological link was postulated, given work exposure in a setting with high risk of transmission in one of them. This case adds insight on the clinical features, the course of disease and management in infants. This 2-month-old infant did not develop any complication from the illness and was among the youngest patients with monkeypox to be treated with tecovirimat. Conclusion As monkeypox infection remains rare in children and may convey a higher risk for severe disease, a high degree of suspicion is warranted for clinicians caring for children. Monkeypox should be included in the differential diagnosis of an unexplained vesiculopustular rash. Finally, tecovirimat as a treatment for monkeypox infection in children was shown here to be safe and effective, even when started late in the evolution.

Surveillance for Ixodes scapularis and Ixodes pacificus ticks and their associated pathogens in Canada, 2020.

Ixodes scapularis and Ixodes pacificus ticks are the principal vectors of the agent of Lyme disease and several other tick-borne diseases in Canada. Tick surveillance data can be used to identify local tick-borne disease risk areas and direct public health interventions. The objective of this article is to describe the seasonal and spatial characteristics of the main Lyme disease vectors in Canada, and the tick-borne pathogens they carry, using passive and active surveillance data from 2020. Passive and active surveillance data were compiled from the National Microbiology Laboratory Branch (Public Health Agency of Canada), provincial and local public health authorities, and eTick (an online, image-based platform). Seasonal and spatial analyses of ticks and their associated pathogens are presented, including infection prevalence estimates. In passive surveillance, I. scapularis (n=7,534) were submitted from all provinces except Manitoba and British Columbia, while I. pacificus (n=718) were submitted only from British Columbia. No ticks were submitted from the Territories. The seasonal distribution of I. scapularis submissions was bimodal, but unimodal for I. pacificus. Four tick-borne pathogens were identified in I. scapularis (Borrelia burgdorferi, Anaplasma phagocytophilum, Babesia microti and Borrelia miyamotoi) and one in I. pacificus (B. miyamotoi). In active surveillance, I. scapularis (n=688) were collected in Ontario, Québec and New Brunswick. Five tick-borne pathogens were identified: B. burgdorferi, A. phagocytophilum, B. microti, B. miyamotoi and Powassan virus. This article provides a snapshot of the distribution of I. scapularis and I. pacificus and their associated human pathogens in Canada in 2020, which can help assess the risk of exposure to tick-borne pathogens in different provinces.

Healthcare-associated infections and antimicrobial resistance in Canadian acute care hospitals, 2017-2021.

Healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) continue to contribute to excess morbidity and mortality among Canadians. This report describes epidemiologic and laboratory characteristics and trends of HAIs and AMR from 2017 to 2021 (Candida auris 2012-2021) using surveillance and laboratory data submitted by hospitals to the Canadian Nosocomial Infection Surveillance Program (CNISP) and by provincial laboratories to the National Microbiology Laboratory (NML). Data collected from 88 Canadian sentinel acute care hospitals between January 1, 2017, and December 31, 2021, for Clostridioides difficile infections (CDI), carbapenemase-producing Enterobacterales (CPE), methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSIs) and vancomycin-resistant Enterococcus (VRE) BSIs. Candida auris (C. auris) surveillance was initiated in 2019 by CNISP and in 2012 by the NML. Case counts, rates, outcomes, molecular characterization and antimicrobial resistance profiles are presented. From 2017 to 2021, increased rates per 10,000 patient days were observed for MRSA BSIs (35%; 0.84-1.13), VRE BSIs (43%; 0.23-0.33) and CPE infections (166%, 0.03-0.08). CDI rates decreased 11% (5.68-5.05). Thirty-one C. auris isolates were identified in Canada from 2012 to 2021, with the majority from Western Canada (68%). From 2017 to 2021, the incidence of MRSA and VRE BSIs, and CPE infections increased in Canadian acute care hospitals participating in a national sentinel network (CNISP) while CDI decreased. Few C. auris isolates were identified from 2012 to 2021. Reporting standardized surveillance data and the consistent application of infection prevention and control practises in acute care hospitals are critical to help decrease the burden of HAIs and AMR in Canada.

Streptococcus pneumoniae serotyping and antimicrobial susceptibility: assessment for vaccine efficacy in Canada after the introduction of PCV13.

Streptococcus pneumoniae continues to be an important bacterial pathogen associated with invasive (e.g. bacteraemia, meningitis) and non-invasive (e.g. community-acquired respiratory tract) infections worldwide. Surveillance studies conducted nationally and globally assist in determining trends over geographical areas and allow comparisons between countries. To characterize invasive isolates of S. pneumoniae in terms of their serotype, antimicrobial resistance, genotype and virulence and to use the serotype data to determine the level of coverage by different generations of pneumococcal vaccines. SAVE (Streptococcus pneumoniae Serotyping and Antimicrobial Susceptibility: Assessment for Vaccine Efficacy in Canada) is an ongoing, annual, national collaborative study between the Canadian Antimicrobial Resistance Alliance (CARE) and the National Microbiology Laboratory, focused on characterizing invasive isolates of S. pneumoniae obtained across Canada. Clinical isolates from normally sterile sites were forwarded by participating hospital public health laboratories to the Public Health Agency of Canada-National Microbiology Laboratory and CARE for centralized phenotypic and genotypic investigation. The four articles in this Supplement provide a comprehensive examination of the changing patterns of antimicrobial resistance and MDR, serotype distribution, genotypic relatedness and virulence of invasive S. pneumoniae obtained across Canada over a 10 year period (2011-2020). The data highlight the evolution of S. pneumoniae under pressure by vaccination and antimicrobial usage, as well as vaccine coverage, allowing both clinicians and researchers nationally and globally to view the current status of invasive pneumococcal infections in Canada.

Clinical Evaluation of the GeneXpert® Xpert® Xpress SARS-CoV-2/Flu/RSV PLUS Combination Test.

The GeneXpert® Xpert® Xpress SARS-CoV-2/Flu/RSV PLUS combination test (PLUS Assay) received Health Canada approval in January 2022. The PLUS Assay is similar to the SARS-CoV-2/Flu/RSV combination test, with modifications to improve assay robustness against circulating and emerging variants. The performance characteristics of the PLUS Assay were assessed at the Lakeridge Health Oshawa Hospital Centre and the National Microbiology Laboratory of Canada. The PLUS Assay was directly compared to the SARS-CoV-2/Flu/RSV combination test using SARS-CoV-2 culture from five variants and remnant clinical specimens collected across the COVID-19 pandemic. This included 50 clinical specimens negative for all pathogens, 110 clinical specimens positive for SARS-CoV-2, Influenza A, Influenza B, RSVA, and/or RSVB and an additional 11 mixed samples to screen for target interactions. The PLUS Assay showed a high percent agreement with the widely used SARS-CoV-2/Flu/RSV combination test. Based on these findings, the PLUS Assay and the Xpert SARS-CoV-2/Flu/RSV combination test results are largely consistent with no observed difference in sensitivity, specificity, or time to result when challenged with various SARS-CoV-2 variants. The reported Ct values provided by the new PLUS Assay was also unchanged, with the exception of a possible 1-2 cycle decrease reported Ct for RSVA across a limited sample size.

Identification of Burkholderia cepacia complex by PCR: A simple way.

USP General Chapter <60> for the detection of Burkholderia cepacia complex (Bcc) members in non-sterile products became official in December 2019. This isolation method requires to confirm the identity of any growth found on Burkholderia cepacia Selective Agar (BCSA) by additional identification tests (refer to the Interpretation section). This article presents a singleplex PCR method to rapidly confirm the membership of any microbial grown on BCSA (& other nutrient medium) in the Bcc group. This method is cost effective as it does not require expensive equipment nor reagents; therefore, it can be easily adopted in the industry. We validated this singleplex PCR Bcc identification method with previously published PCR primers with an expanded panel of 37 clinical and environmental Bcc isolates. The sources and repositories of these Bcc isolates include contaminated health products and medical devices, patients infected with cystic fibrosis, the National Microbiology Laboratory (NML) internal bank and the American type culture collection (ATCC). All 37 isolates that belong to the Bcc have been tested positive using our confirmatory identification method. Twenty-two negative controls including 4 isolates belonging to the genus Burkholderia have been tested negative as expected. Our work indicates this singleplex PCR is an efficient confirmatory method for a Bcc identification, and it can successfully supplement USP chapter <60> in Bcc isolate identification found in pharmaceutical products.

Antimicrobial susceptibilities of Neisseria gonorrhoeae in Canada, 2020.

The Gonococcal Antimicrobial Surveillance Programme is a passive surveillance system that has monitored antimicrobial resistance in Neisseria gonorrhoeae in Canada since the 1980s. This article summarizes the demographics, antimicrobial resistances and NG-MAST (N. gonorrhoeae multiantigen sequence typing) for cultures collected in 2020. The National Microbiology Laboratory (NML) in Winnipeg received resistant N. gonorrhoeae cultures from provincial and territorial public health laboratories. Agar dilution was used to determine the minimum inhibitory concentrations to ten antimicrobials for all cultures received at NML, according to Clinical and Laboratory Standards Institute guidelines. The NG-MAST typing was also determined for each culture. A total of 3,130 N. gonorrhoeae cases were cultured across Canada in 2020; a 36% decrease from 2019 (n=4,859). The level of decreased susceptibility to cefixime increased significantly between 2016 and 2020 to 2.8% (p=0.0054). Decreased susceptibility to ceftriaxone declined significantly between 2016 (1.8%) and 2020 to 0.9% (p=0.001), and there was no significant change with azithromycin between 2016 (7.2%) and 2020 (6.1%). The proportion of cultures with an azithromycin minimum inhibitory concentrations of ≥1 mg/L increased significantly from 11.6% in 2016 to 15.3% in 2020 (p=0.0017). The most common NG-MAST type in Canada for 2020 was sequence type (ST)-11461, while ST-12302 was most commonly associated with azithromycin resistance and ST-16639 with cephalosporin decreased susceptibility. Antimicrobial resistance in N. gonorrhoeae remains an important public health concern and continued surveillance is imperative to monitor trends to ensure the recommended therapies will be the most effective.

Overview of Canada's Antimicrobial Resistance Network (AMRNet): A data-driven One Health approach to antimicrobial resistance surveillance.

The Antimicrobial Resistance Network (AMRNet) is a laboratory-based antimicrobial resistance (AMR) surveillance system under development at the Public Health Agency of Canada's (PHAC's) National Microbiology Laboratory. The AMRNet surveillance system captures information on antimicrobial susceptibility testing from clinical and veterinary laboratories including both public and private facilities. In the future, the AMRNet system will also capture relevant data from existing PHAC surveillance systems for AMR including the Canadian Integrated Program for Antimicrobial Resistance Surveillance, the Canadian Nosocomial Infection Surveillance Program and the Enhanced Surveillance of Antimicrobial-Resistant Gonorrhea program, and contribute to the Canadian Antimicrobial Resistance Surveillance System. AMRNet's integrated "One Health" approach will allow health professionals and researchers to take a multi-dimensional perspective of AMR in both human and animal health in Canada and will make Canada a leader in AMR surveillance. AMRNet is a collaboration between PHAC, provincial and territorial public health organizations as well as clinical and veterinary laboratories across the country. As part of a phased rollout, AMRNet is now collecting human clinical data from three provinces, from both inpatients and outpatients. Ultimately, AMRNet aims to capture all antimicrobial susceptibility testing results from all bacterial and fungal pathogens across Canada. This article describes the AMRNet surveillance system, including program objectives, system structure and the data collected. The integration of human and animal data in AMRNet will inform One Health responses to AMR issues. The capacity to collect and to disseminate data to stakeholders in real time is a critical step to addressing emerging AMR issues in Canada.

Evaluation of the performance of multiple immunoassay diagnostic platforms on the National Microbiology Laboratory SARS-CoV-2 National Serology Panel.

Serological assays designed to detect SARS-CoV-2 antibodies are being used in serological surveys and other specialized applications. As a result, and to ensure that the outcomes of serological testing meet high quality standards, evaluations are required to assess the performance of these assays and the proficiency of laboratories performing them. A panel of 60 plasma/serum samples from blood donors who had reverse transcriptase-polymerase chain reaction (RT-PCR) confirmed SARS-CoV-2 infections and 21 SARS-CoV-2 negative samples were secured and distributed to interested laboratories within Canada (n = 30) and the United States (n = 1). Participating laboratories were asked to provide details on the diagnostic assays used, the platforms the assays were performed on, and the results obtained for each panel sample. Laboratories were blinded with respect to the expected outcomes. The performance of the different assays evaluated was excellent, with the high-throughput platforms of Roche, Ortho, and Siemens demonstrating 100% sensitivity. Most other high-throughput platforms had sensitivities of >93%, with the exception of the IgG assay using the Abbott ARCHITECT which had an average sensitivity of only 87%. The majority of the high-throughput platforms also demonstrated very good specificities (>97%). This proficiency study demonstrates that most of the SARS-CoV-2 serological assays utilized by provincial public health or hospital laboratories in Canada have acceptable sensitivity and excellent specificity.

Surveillance for Ixodes scapularis and Ixodes pacificus ticks and their associated pathogens in Canada, 2019.

The primary vectors of the agent of Lyme disease in Canada are Ixodes scapularis and Ixodes pacificus ticks. Surveillance for ticks and the pathogens they can transmit can inform local tick-borne disease risk and guide public health interventions. The objective of this article is to characterize passive and active surveillance of the main Lyme disease tick vectors in Canada in 2019 and the tick-borne pathogens they carry. Passive surveillance data were compiled from the National Microbiology Laboratory Branch and provincial public health data sources. Active surveillance was conducted in selected sentinel sites in all provinces. Descriptive analysis of ticks submitted and infection prevalence of tick-borne pathogens are presented. Seasonal and spatial trends are also described. In passive surveillance, specimens of I. scapularis (n=9,858) were submitted from all provinces except British Columbia and I. pacificus (n=691) were submitted in British Columbia and Alberta. No ticks were submitted from the territories. The seasonal distribution pattern was bimodal for I. scapularis adults, but unimodal for I. pacificus adults. Borrelia burgdorferi was the most prevalent pathogen in I. scapularis (18.8%) and I. pacificus (0.3%). In active surveillance, B. burgdorferi was identified in 26.2% of I. scapularis; Anaplasma phagocytophilum in 3.4% of I. scapularis, and Borrelia miyamotoi and Powassan virus in 0.5% or fewer of I. scapularis. These same tick-borne pathogens were not found in the small number of I. pacificus tested. This surveillance article provides a snapshot of the main Lyme disease vectors in Canada and their associated pathogens, which can be used to monitor emerging risk areas for exposure to tick-borne pathogens.

Epidemiology of invasive meningococcal disease in Canada, 2012-2019.

A variety of routine childhood and adolescent meningococcal vaccination programs using monovalent (serogroup C) and quadrivalent (A, C, Y, W) conjugate vaccines have been implemented in Canada since 2002, resulting in a decrease in invasive meningococcal disease (IMD) incidence, particularly in serogroup C. Meningococcal vaccines have also been used for outbreak response, including the multicomponent vaccine serogroup B vaccine. This report describes the epidemiology of IMD in Canada from 2012 to 2019. Case data were obtained from the National Enhanced IMD Surveillance System between January 1, 2012 and December 31, 2019. Isolates were sent to the National Microbiology Laboratory for confirmation of serogroup and further studies including phenotype and clonal complex identification. A total of 983 cases of IMD were reported between 2012 and 2019. Overall, the age-adjusted incidence of IMD from 2012 to 2019 was 0.34 cases per 100,000 population per year when standardized to the Canadian 2011 population age distribution (95% CI: 0.32-0.36). Infants younger than one year of age had the highest average age-specific incidence rate (3.6 cases per 100,000 population per year, 95% CI: 2.8-4.3). The highest age-adjusted incidence rate was associated with serogroup B (0.17 cases per 100, 000 population per year, 95% CI: 0.16-0.19). Prior to 2015, most invasive serogroup W isolates were identified as clonal complex 22 (ST-22 CC) and the increase in serogroup W in Canada in recent years has been associated with the replacement of the endemic ST-22 CC with the hyper-virulent ST-11 CC. Invasive meningococcal disease is a rare but severe infection in Canada that mostly affects the very young. Serogroup B continues to account for the greatest proportion of disease. Serogroup W associated with ST-11 CC is becoming a growing contributor of disease in all age groups not protected by serogroup W-containing vaccines.

COVID-19 sample management: experiences of Harare City, 2021.

COVID-19 sample management is pivotal in controlling the pandemic. Results of 28/45 (62.2%) cases identified at a high school COVID-19 outbreak in Harare’s Northern district were not reported within the recommended 24 hours of notification. This leads to delayed patient management. We evaluated the sample management system for COVID-19 in Harare City. A descriptive cross-sectional study was conducted in Harare City. Health care workers involved in COVID-19 sample management at a high school outbreak in the Northern district namely clinicians, laboratory, environmental and administrative personnel were purposively sampled. Interviewer-administered questionnaires were used to collect data. Quantitative data were analyzed using Epi info version 7. Medians and proportions were generated. A 3-point Likert Scale was used to measure knowledge levels of health care workers on COVID-19 sample management. Thirty health care workers were interviewed and females were 20/30 (66%). Participants had not been trained in sample management. Overall knowledge level was good for 7/30 (23%) of the participants. Of the samples collected, 156/451 (34.6%) were wrongly sent to the national microbiology laboratory and 53/156 (34.0%) of the results were received. Sample management of COVID-19 samples in Harare City was found to affect patient management because of poor knowledge of healthcare workers, lack of transportation and communication means. The need for training cadres involved in the management process and availing adequate resources can improve turnaround time of results hence patient management.

Serologic testing for Bartonella in Manitoba, Canada, 2010-2020: a retrospective case series.

Background:Bartonella are gram-negative bacilli not identified by routine bacterial culture. The objectives of this study were to review the results of all serologic testing for Bartonella ordered in Manitoba, Canada, and to review cases with positive test results among adults to assess species identification, risk factors, clinical manifestations and outcomes.Methods:This retrospective study included all Bartonella serologic tests ordered in Manitoba and performed at the National Microbiology Laboratory, Winnipeg, from Jan. 1, 2010, until Dec. 31, 2020. We analyzed the aggregate data for all serologic tests for Bartonella for patients of all ages. We reviewed the charts of adult (age ≥ 18 yr) patients with serologic positivity for Bartonella who had a medical chart at 1 of Winnipeg’s 2 largest hospitals (Health Sciences Centre and St. Boniface Hospital) to extract clinical and demographic data and create a case series. Descriptive statistics were performed.Results:During the study period, 1014 Bartonella serologic tests were ordered in adult and pediatric patients, of which 24 (2.4%) gave a positive result. Sixteen adults (12 men and 4 women; mean age 48 yr) seen at a participating hospital had a positive result. Molecular species-level identification occurred on explanted cardiac valves in 5 (31%) of the 16 cases; B. quintana was identified in all 5. Six patients (38%) were diagnosed with probable B. quintana infection, for a total of 11 B. quintana cases (69%); 8 (73%) of the 11 had endocarditis. Four cases of B. quintana infection (36%) were associated with rural residence. Four cases (25%) of probable B. henselae were identified; 2 patients had fever and lymphadenopathy, and 2 had endocarditis. The remaining patient was deemed to have a false-positive result as his B. henselae titre was at the threshold for positivity, his B. quintana serologic test gave a negative result, and his clinical syndrome was not suggestive of Bartonella infection. Two patients died; both had multivalvular B. quintana endocarditis with ruptured intracranial mycotic aneurysms.Interpretation:Bartonella quintana was a common cause of Bartonella serologic positivity among adults in Manitoba in 2010–2020 and was associated with endocarditis and systemic embolization. As B. quintana is transmitted by body lice, active case finding for people who lack suitable housing, both in urban and rural settings, should prioritize those with elevated Bartonella titres to receive echocardiography and detect endocarditis before systemic embolization occurs.

High level of plasma TILRR protein is associated with faster HIV seroconversion.

SummaryBackgroundTILRR (Toll-like Interleukin-1 Receptor Regulator) is a modulator of many genes in NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) signaling. It promotes the production of inflammatory mediators and the migration of immune cells. Recently, we showed that TILRR protein circulates in human blood. Thus, it could influence systemic inflammation. Systemic and mucosal inflammations increase the susceptibility to HIV infection. In this study, we analyzed the TILRR protein levels of the archived plasma samples of women enrolled in the Pumwani cohort to determine whether the plasma TILRR protein levels before seroconversion are correlated with differential risk of HIV seroconversion.MethodsTILRR protein of 941 archived HIV negative plasma samples from 390 women who were HIV negative at the cohort enrollment was quantified with an in-house developed multiplex bead array method. Proinflammatory cytokines/chemokines were measured using a 14-plex bead array method. Spearman rank correlation analysis was used to determine the correlation between plasma TILRR protein and proinflammatory cytokines/chemokines. Kaplan-Meier survival analysis was conducted to evaluate whether the median plasma TILRR protein levels correlate with increased risk of HIV seroconversion.FindingsThe level of plasma TILRR protein was positively correlated with plasma IL-1β (rho: 0.2593, p<0.0001), MCP-1 (rho: 0.2377, p<0.0001), and IL-17A (rho: 0.1225, p=0.0216). Women with median plasma TILRR protein levels ≥100 ng/ml seroconverted significantly faster than women with plasma TILRR protein levels <100 ng/ml (log-rank= 100.124, p<0.0001; relative risk= 3.72 and odds ratio= 15.29). Furthermore, the factors causing genital inflammation, such as STIs (sexually transmitted infections), vaginal discharge, and genital ulcers were not statistically significantly different among women with different median plasma TILRR protein levels.InterpretationThe high plasma TILRR protein levels are highly correlated with several plasma proinflammatory cytokines/chemokines. High median plasma TILRR protein (≥100 ng/ml) strongly predicted an increased risk of HIV seroconversion. Reducing plasma TILRR protein levels may reduce the risk of HIV acquisition.FundingThe study was funded by an operating grant from the Canadian Institutes of Health Research (CIHR), operating grant-PA: CHVI Vaccine Discovery and Social Research (http://www.cihr-irsc.gc.ca/e/193.html), and National Microbiology Laboratory of Canada.

Addressing Privacy Concerns in Sharing Viral Sequences and Minimum Contextual Data in a Public Repository During the COVID-19 Pandemic.

COVID-19 was declared to be a pandemic in March 2020 by the World Health Organization. Timely sharing of viral genomic sequencing data accompanied by a minimal set of contextual data is essential for informing regional, national, and international public health responses. Such contextual data is also necessary for developing, and improving clinical therapies and vaccines, and enhancing the scientific community’s understanding of the SARS-CoV-2 virus. The Canadian COVID-19 Genomics Network (CanCOGeN) was launched in April 2020 to coordinate and upscale existing genomics-based COVID-19 research and surveillance efforts. CanCOGeN is performing large-scale sequencing of both the genomes of SARS-CoV-2 virus samples (VirusSeq) and affected Canadians (HostSeq). This paper addresses the privacy concerns associated with sharing the viral sequence data with a pre-defined set of contextual data describing the sample source and case attribute of the sequence data in the Canadian context. Currently, the viral genome sequences are shared by provincial public health laboratories and their healthcare and academic partners, with the Canadian National Microbiology Laboratory and with publicly accessible databases. However, data sharing delays and the provision of incomplete contextual data often occur because publicly releasing such data triggers privacy and data governance concerns. The CanCOGeN Ethics and Governance Expert Working Group thus has investigated several privacy issues cited by CanCOGeN data providers/stewards. This paper addresses these privacy concerns and offers insights primarily in the Canadian context, although similar privacy considerations also exist in other jurisdictions. We maintain that sharing viral sequencing data and its limited associated contextual data in the public domain generally does not pose insurmountable privacy challenges. However, privacy risks associated with reidentification should be actively monitored due to advancements in reidentification methods and the evolving pandemic landscape. We also argue that during a global health emergency such as COVID-19, privacy should not be used as a blanket measure to prevent such genomic data sharing due to the significant benefits it provides towards public health responses and ongoing research activities.