Invasive pneumococcal disease surveillance in Canada, 2021-2022.

Background: 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. Methods: 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. Results: 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). Conclusion: 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.

Background: 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. Methods: 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. Results: 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. Conclusion: 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.

Responding to and managing multijurisdictional outbreaks of COVID-19 in Canadian industrial worksite/work camp settings.

SETTING: Early in the COVID-19 pandemic, the Public Health Agency of Canada (PHAC) and provincial/territorial (P/T) public health identified the need for a coordinated response to complex multijurisdictional COVID-19 outbreaks. The first large multijurisdictional industrial worksite COVID-19 outbreak highlighted the risk of transmission within these congregate work settings, the risk of transmission to the broader community(ies), and the need to develop setting-specific outbreak response frameworks. INTERVENTION: PHAC assembled a team to provide national outbreak support for multijurisdictional COVID-19 outbreaks in May 2020. The COVID-19 Outbreak Response Unit (ORU) worked with P/T partners to develop guiding principles for outbreak response and outbreak investigation processes, guidance documents, and investigation tools (e.g., minimum data elements and questionnaires). OUTCOMES: The ORU, P/T partners, and onsite industrial worksite health and safety staff leveraged outbreak investigation guidelines, industrial worksite outbreak process documents (including minimum data elements), and enhanced case questionnaires to respond to multiple COVID-19 outbreak investigations in industrial worksites. Clear roles/responsibilities and processes, along with standardized data, allowed for more efficient outbreak investigations and earlier implementation of mitigation measures. IMPLICATIONS: Multijurisdictional COVID-19 outbreaks highlighted the importance of public health collaboration with industry partners onsite. The assembly of a national outbreak response team was important to facilitate information sharing and provide technical support. Lessons learned and recommendations on outbreak preparation, detection, management, and communication are included to enhance a response framework applicable to future emerging or re-emerging pathogens with epidemic and/or pandemic potential.

RéSUMé: CONTEXTE: Au début de la pandémie de COVID-19, l'Agence de la santé publique du Canada (ASPC) et les autorités provinciales/territoriales de santé publique ont reconnu la nécessité d'une réponse coordonnée en cas d'éclosions complexes multi-juridictionnelles de COVID-19. La première grande éclosion multi-juridictionnelle de COVID-19 dans un chantier industriel a mis en évidence le risque de transmission dans ces milieux de travail collectifs, le risque de transmission à l'ensemble de la (des) communauté(s) et la nécessité d'élaborer des cadres d'intervention en cas d'éclosion spécifiques aux types de milieux. INTERVENTION: L'ASPC a formé une équipe chargée de soutenir la réponse nationale contre les éclosions multi-juridictionnelles de COVID-19 en mai 2020. L'Unité d'intervention en cas d'éclosion (UIE) de COVID-19 a collaboré avec des partenaires provinciaux et territoriaux pour élaborer des principes de référence pour la lutte contre les éclosions de COVID-19 et des processus d'enquête sur les éclosions, des documents d'orientation et des outils d'enquête (p.ex. des éléments de données minimales et des questionnaires). RéSULTATS: L'UIE, les provinces et territoires et le personnel chargé de la santé et sécurité du travail sur le site se sont appuyés sur des principes de référence aux enquêtes sur les éclosions, les documents de processus d'enquête sur les éclosions dans les sites industriels, y compris les éléments de données minimales et le questionnaire détaillé sur les cas, pour répondre à multiples enquêtes d'éclosions de COVID-19 dans les sites industriels. Des rôles/responsabilités et des processus clairs, ainsi que des données standardisées, ont permis de mener des enquêtes plus efficaces sur les éclosions et de mettre en œuvre plus rapidement des mesures d'atténuation. IMPLICATIONS: Les éclosions multi-juridictionnelles de COVID-19 ont mis en évidence l'importance de la collaboration entre les autorités de santé publique et les partenaires industriels sur site. La constitution d'une équipe nationale d'intervention en cas d'éclosion a été importante pour faciliter le partage des informations et fournir un soutien technique. Les connaissances acquises et les recommandations sur la préparation, la détection, la gestion et la communication des éclosions sont incluses afin d'améliorer le cadre de réponse aux futurs agents pathogènes émergents ou ré-émergents ayant un potentiel épidémique et/ou pandémique.

Multijurisdictional outbreak of COVID-19 associated with a wake/funeral event in a northern Saskatchewan First Nations community.

Background: Sixty-eight laboratory-confirmed cases of the coronavirus disease 2019 (COVID-19) (12 in Alberta [AB], 56 in Saskatchewan [SK]) were linked to a gathering at a hospital in Alberta on June 1-4, 2020, and a wake/funeral in a First Nations community in northern Saskatchewan on June 9-11, 2020. Objective: The objectives were to provide a comprehensive description of the epidemiology of the outbreak and describe the chains of transmission to inform the hypothesis that there were multiple introductions of COVID-19 at the wake/funeral. Methods: Case investigation and contact tracing was conducted by local public health in AB and SK. The Public Health Agency of Canada conducted a centralized case analysis. An epidemic curve and a Gantt chart for period of communicability were created to support or refute whether there had been multiple introductions of COVID-19 at the wake/funeral. Results: Illness onset dates ranged from May 31 to July 1, 2020. Ages ranged from 2 to 80 years (median age=43 years). Five cases were hospitalized; there were no deaths. The available case exposure information supports the hypothesis that there had been multiple introductions of COVID-19 at the wake/funeral. Public health authorities in AB and SK declared the outbreak over on July 20, 2020; based on two incubation periods (i.e. 28 days) following the illness onset of the last primary case. Conclusion: During multijurisdictional outbreaks, data sharing, coordination across health authorities and centralized analysis is essential to understanding the events that lead to the outbreak and possible hypotheses around chains of transmission.

The need for linked genomic surveillance of SARS-CoV-2.

Genomic surveillance during the coronavirus disease 2019 (COVID-19) pandemic has been key to the timely identification of virus variants with important public health consequences, such as variants that can transmit among and cause severe disease in both vaccinated or recovered individuals. The rapid emergence of the Omicron variant highlighted the speed with which the extent of a threat must be assessed. Rapid sequencing and public health institutions' openness to sharing sequence data internationally give an unprecedented opportunity to do this; however, assessing the epidemiological and clinical properties of any new variant remains challenging. Here we highlight a "band of four" key data sources that can help to detect viral variants that threaten COVID-19 management: 1) genetic (virus sequence) data; 2) epidemiological and geographic data; 3) clinical and demographic data; and 4) immunization data. We emphasize the benefits that can be achieved by linking data from these sources and by combining data from these sources with virus sequence data. The considerable challenges of making genomic data available and linked with virus and patient attributes must be balanced against major consequences of not doing so, especially if new variants of concern emerge and spread without timely detection and action.

Multistate Outbreak of Listeriosis Associated with Packaged Leafy Green Salads, United States and Canada, 2015-2016.

We investigated an outbreak of listeriosis detected by whole-genome multilocus sequence typing and associated with packaged leafy green salads. Nineteen cases were identified in the United States during July 5, 2015-January 31, 2016; isolates from case-patients were closely related (median difference 3 alleles, range 0-16 alleles). Of 16 case-patients interviewed, all reported salad consumption. Of 9 case-patients who recalled brand information, all reported brands processed at a common US facility. The Public Health Agency of Canada simultaneously investigated 14 cases of listeriosis associated with this outbreak. Isolates from the processing facility, packaged leafy green salads, and 9 case-patients from Canada were closely related to US clinical isolates (median difference 3 alleles, range 0-16 alleles). This investigation led to a recall of packaged leafy green salads made at the processing facility. Additional research is needed to identify best practices and effective policies to reduce the likelihood of Listeria monocytogenes contamination of fresh produce.

Outbreak of Escherichia coli O157:H7 Infections Linked to Aged Raw Milk Gouda Cheese, Canada, 2013.

Between 12 July and 29 September 2013, 29 individuals in five Canadian provinces became ill following infection with the same strain of Escherichia coli O157:H7 as defined by molecular typing results. Five case patients were hospitalized, and one died. Twenty-six case patients (90%) reported eating Gouda cheese originating from a dairy plant in British Columbia. All of the 22 case patients with sufficient product details available reported consuming Gouda cheese made with raw milk; this cheese had been produced between March and July 2013 and was aged for a minimum of 60 days. The outbreak strain was isolated from the implicated Gouda cheese, including one core sample obtained from an intact cheese wheel 83 days after production. The findings indicate that raw milk was the primary source of the E. coli O157:H7, which persisted through production and the minimum 60-day aging period. This outbreak is the third caused by E. coli O157:H7 traced to Gouda cheese made with raw milk in North America. These findings provide further evidence that a 60-day ripening period cannot ensure die-off of pathogens that might be present in raw milk Gouda cheese after production and have triggered an evaluation of processing conditions, physicochemical parameters, and options to mitigate the risk of E. coli O157:H7 infection associated with raw milk Gouda cheese produced in Canada.

Operational evaluation of rapid diagnostic testing for Ebola Virus Disease in Guinean laboratories.

BACKGROUND: Rapid Diagnostic Tests (RDTs) for Ebola Virus Disease (EVD) at the point of care have the potential to increase access and acceptability of EVD testing and the speed of patient isolation and secure burials for suspect cases. A pilot program for EVD RDTs in high risk areas of Guinea was introduced in October 2015. This paper presents concordance data between EVD RDTs and PCR testing in the field as well as an assessment of the acceptability, feasibility, and quality assurance of the RDT program. METHODS AND FINDINGS: Concordance data were compiled from laboratory surveillance databases. The operational measures of the laboratory-based EVD RDT program were evaluated at all 34 sentinel sites in Guinea through: (1) a technical questionnaire filled by the lab technicians who performed the RDTs, (2) a checklist filled by the evaluator during the site visits, and (3) direct observation of the lab technicians performing the quality control test. Acceptability of the EVD RDT was good for technicians, patients, and families although many technicians (69.8%) expressed concern for their safety while performing the test. The feasibility of the program was good based on average technician knowledge scores (6.6 out of 8) but basic infrastructure, equipment, and supplies were lacking. There was much room for improvement in quality assurance of the program. CONCLUSIONS: The implementation of new diagnostics in weak laboratory systems requires general training in quality assurance, biosafety and communication with patients in addition to specific training for the new test. Corresponding capacity building in terms of basic equipment and a long-term commitment to transfer supervision and quality improvement to national public health staff are necessary for successful implementation.

Canadian Consumer Food Safety Practices and Knowledge: Foodbook Study.

Understanding consumers' food safety practices and knowledge supports food safety education for the prevention of foodborne illness. The objective of this study was to describe Canadian consumer food safety practices and knowledge. This study identifies demographic groups for targeted food safety education messaging and establishes a baseline measurement to assess the effectiveness of food safety interventions over time. Questions regarding consumer food safety practices and knowledge were included in a population-based telephone survey, Foodbook, conducted from November 2014 to March 2015. The results were analyzed nationally by age group and by gender. The results showed that approximately 90% of Canadians reported taking the recommended cleaning and separating precautions when handling raw meat to prevent foodborne illness. Only 29% of respondents reported using a food thermometer when cooking any meat, and even fewer (12%) reported using a food thermometer for small cuts of meat such as chicken pieces. The majority (>80%) of Canadians were aware of the foodborne illness risks related to chicken and hamburger, but fewer (<40%) were aware of the risks related to frozen chicken nuggets, alfalfa sprouts, soft unpasteurized cheese, and unpasteurized juices. Generally, men were less likely to follow cooking instructions on packaging and took fewer steps to prevent cross-contamination than women. The youngest (18 to 29 years) age group was less likely to take steps to avoid cross-contamination and was less aware of the risks associated with eating an undercooked hamburger. The oldest (60+ years) respondents were less likely to be aware of the risks associated with raw eggs, alfalfa sprouts, and unpasteurized juice than the middle (30 to 59 years) age group. As a priority, food safety education in Canada should focus on increasing people's awareness of high-risk foods, specifically foods for which the awareness of risk found in this study was low; targeting messaging to demographic groups as appropriate; and promoting the use of food thermometers when cooking meat and poultry.

Notes from the Field: Outbreak of Listeriosis Associated with Consumption of Packaged Salad - United States and Canada, 2015-2016.

In September 2015, PulseNet, the national molecular subtyping network for foodborne disease surveillance, identified a cluster of Listeria monocytogenes (Listeria) clinical isolates indistinguishable by two-enzyme pulsed-field gel electrophoresis (PFGE) pattern combination and highly related by whole-genome multilocus sequence typing (wgMLST). A case was defined as isolation of Listeria with the outbreak PFGE pattern and highly related by wgMLST with an isolation date on or after July 5, 2015, the isolate date of the earliest case in this cluster.

Multi-laboratory evaluation of the rapid genoserotyping array (SGSA) for the identification of Salmonella serovars.

Salmonella serotyping is an essential first step for identification of isolates associated with disease outbreaks. The Salmonella genoserotyping array (SGSA) is a microarray-based alternative to standard serotyping designed to rapidly identify 57 of the most commonly reported serovars through detection of the genes encoding surface O and H antigens and reporting the corresponding serovar in accordance with the existing White-Kaufmann-Le Minor serotyping scheme. In this study, we evaluated the SGSA at 4 laboratories in 3 countries by testing 1874 isolates from human and non-human sources. The SGSA correctly identified 96.7% of isolates from the target 57 serovars. For the prevalent and clinically important Salmonella serovars Enteritidis and Typhimurium, test specificity and sensitivity were greater than 98% and 99%, respectively. Due to its high-throughput nature, the SGSA is a rapid and cost-effective alternative to standard serotyping for identifying the most prevalent serovars of Salmonella.

The host-range, genomics and proteomics of Escherichia coli O157:H7 bacteriophage rV5.

BACKGROUND: Bacteriophages (phages) have been used extensively as analytical tools to type bacterial cultures and recently for control of zoonotic foodborne pathogens in foods and in animal reservoirs. METHODS: We examined the host range, morphology, genome and proteome of the lytic E. coli O157 phage rV5, derived from phage V5, which is a member of an Escherichia coli O157:H7 phage typing set. RESULTS: Phage rV5 is a member of the Myoviridae family possessing an icosahedral head of 91 nm between opposite apices. The extended tail measures 121 x 17 nm and has a sheath of 44 x 20 nm and a 7 nm-wide core in the contracted state. It possesses a 137,947 bp genome (43.6 mol%GC) which encodes 233 ORFs and six tRNAs. Until recently this virus appeared to be phylogenetically isolated with almost 70% of its gene products ORFans. rV5 is closely related to coliphages Delta and vB-EcoM-FY3, and more distantly related to Salmonella phages PVP-SE1 and SSE-121, Cronobacter sakazakii phage vB_CsaM_GAP31, and coliphages phAPEC8 and phi92. A complete shotgun proteomic analysis was carried out on rV5, extending what had been gleaned from the genomic analyses. Host range studies revealed that rV5 is active against several other E. coli.

Escherichia coli O157:H7 typing phage V7 is a T4-like virus.

The complete genome sequence of the Escherichia coli O157:H7 typing phage V7 was determined. Its double-stranded DNA genome is 166,452 bp long, encoding 273 proteins and including 11 tRNAs. This virus belongs to the genus T4-like viruses within the subfamily Tevenvirinae, family Myoviridae.

Rapid genoserotyping tool for classification of Salmonella serovars.

We have developed a Salmonella genoserotyping array (SGSA) which rapidly generates an antigenic formula consistent with the White-Kauffmann-Le Minor scheme, currently the gold standard for Salmonella serotyping. A set of 287 strains representative of 133 Salmonella serovars was assembled to validate the array and to test the array probes for accuracy, specificity, and reproducibility. Initially, 76 known serovars were utilized to validate the specificity and repeatability of the array probes and their expected probe patterns. The SGSA generated the correct serovar designations for 100% of the known subspecies I serovars tested in the validation panel and an antigenic formula consistent with that of the White-Kauffmann-Le Minor scheme for 97% of all known serovars tested. Once validated, the SGSA was assessed against a blind panel of 100 Salmonella enterica subsp. I samples serotyped using traditional methods. In summary, the SGSA correctly identified all of the blind samples as representing Salmonella and successfully identified 92% of the antigens found within the unknown samples. Antigen- and serovar-specific probes, in combination with a pepT PCR for confirmation of S. enterica subsp. Enteritidis determinations, generated an antigenic formula and/or a serovar designation consistent with the White-Kauffmann-Le Minor scheme for 87% of unknown samples tested with the SGSA. Future experiments are planned to test the specificity of the array probes with other Salmonella serovars to demonstrate the versatility and utility of this array as a public health tool in the identification of Salmonella.

The O28 Antigen Gene Clusters of Salmonella enterica subsp. enterica Serovar Dakar and Serovar Pomona Are Different.

A 10 kb O-antigen gene cluster was sequenced from a Salmonella enterica subsp. enterica Dakar O28 reference strain and from two S. Pomona serogroup O28 isolates. The two S. Pomona O antigen gene clusters showed only moderate identity with the S. Dakar O28 gene cluster, suggesting that the O antigen oligosaccharides may contain one or more sugars conferring the O28 epitope but may otherwise be different. These novel findings are absolutely critical for the correct interpretation of molecular serotyping assays targeting genes within the O antigen gene clusters of these Salmonella serotypes and suggest the possibility that the O antigen gene clusters of other Salmonella serovars may also be heterogenous.

Escherichia coli O123 O antigen genes and polysaccharide structure are conserved in some Salmonella enterica serogroups.

The serotyping of O and H antigens is an important first step in the characterization of Salmonella enterica. However, serotyping has become increasingly technically demanding and expensive to perform. We have therefore sequenced additional S. enterica O antigen gene clusters to provide information for the development of DNA-based serotyping methods. Three S. enterica isolates had O antigen gene clusters with homology to the Escherichia coli O123 O antigen region. O antigen clusters from two serogroup O58 S. enterica strains had approximately 85 % identity with the E. coli O123 O antigen region over their entire length, suggesting that these Salmonella and E. coli O antigen regions evolved from a common ancestor. The O antigen cluster of a Salmonella serogroup O41 isolate had a lower level of identity with E. coli O123 over only part of its O antigen DNA cluster sequence, suggesting a different and more complex evolution of this gene cluster than those in the O58 strains. A large part of the Salmonella O41 O antigen DNA cluster had very close identity with the O antigen cluster of an O62 strain. This region of DNA homology included the wzx and wzy genes. Therefore, molecular serotyping tests using only the O41 or O62 wzx and wzy genes would not differentiate between the two serogroups. The E. coli O123 O-antigenic polysaccharide and its repeating unit were characterized, and the chemical structure for E. coli O123 was entirely consistent with the O antigen gene cluster sequences of E. coli O123 and the Salmonella O58 isolates. An understanding of both the genetic and structural composition of Salmonella and E. coli O antigens is necessary for the development of novel molecular methods for serotyping these organisms.

Preparation and characterization of anti-phage serum.

This chapter describes a method for the generation of polyclonal antibodies against bacteriophages and how these may be assayed immunochemically and biologically.

Generalized transduction by lytic bacteriophages.

As interest in lytic phages as antimicrobial therapies or as treatments to reduce environmental contamination with pathogenic bacteria has increased, so has the need to determine if the use of lytic phages may lead to dissemination of virulence factors through generalized transduction, as occurs with temperate phages. Here we describe simple methods we have developed to determine if a lytic phage, rV5, can mediate generalized transduction in Escherichia coli O157:H7. These sensitive methods can be easily adapted to study generalized transduction between virulent and avirulent strains of bacteria.

Methodologies towards the development of an oligonucleotide microarray for determination of Salmonella serotypes.

A DNA-based microarray designed to detect somatic (O) and flagellar (H) antigens present in the five most commonly isolated Salmonella serovars within Canada was developed as an alternative to the traditional Kauffmann-White serotyping scheme currently used to serotype salmonellae. Short oligonucleotide probes were designed based on publicly available sequence data of selected genes responsible for O and H antigen biosynthesis. These targets included: antigen-specific sequences within the flagella (H) antigen phase 1 (fliC) and phase 2 (fljB) genes and somatic (O) antigen biosynthesis genes within the rfb cluster (Groups B--rfbJ, C1--wbaA, C2--rfbJ, D1--rfbS). A prototype microarray with 117 O and H antigen-specific probes and controls was used to assess probe performance against two pools of gene target PCR amplicons. A set of 31 of these antigen-specific probes (8 O and 23 H) with high specific signal and low non-specific signal were selected based on t-test (p-value <0.01) and log(2) ratio distribution analysis to create a prototype microarray. The microarray was tested against 16 Salmonella strains of known serotype. Based on the strains tested in this study, these probes successfully identified and differentiated 11 of the 12 antigens targeted. The prototype DNA-based typing microarray described here has the potential to be an automated alternative to the traditional antigen-antibody serotyping scheme currently used for Salmonella.