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.

The objective of this annual surveillance report is to provide a summary of the serotypes and antimicrobial resistance associated with IPD in Canada in 2021 and 2022.

Surveillance program
Canadian surveillance of IPD consists of a passive laboratorybased system where invasive isolates from the provincial and territorial public health laboratories are sent to either the National Microbiology Laboratory (NML) in Winnipeg, Manitoba, the Alberta Public Health Laboratory (ProvLab), or the Laboratoire de santé publique du Québec (LSPQ) for serotyping.There were 1,999 IPD isolates reported in 2021 and 3,775 isolates reported in 2022 (Table 1 and Table 2), including isolates serotyped by LSPQ (n=353, 2021; n=708, 2022) and ProvLab (n=302, 2021; n=643, 2022).An expansion of IPD surveillance in Québec occurred in 2019 to include all invasive strains.Sterile clinical isolation sites include blood, cerebrospinal fluid, peritoneal, pericardial or joint fluid, internal body sites, and deep tissue, including surgical or biopsy samples.For this report, isolates from pleural fluid (empyema) are included, despite not meeting the current national case definition for invasive disease, as they are widely considered as invasive in other jurisdictions (3).

Isolate testing
Invasive pneumococcal disease isolates were screened using bile solubility and optochin disc susceptibility at NML until October 2022, when bile solubility was discontinued (Oxoid) (14).Serotyping of IPD at LSPQ and ProvLab Alberta was performed by the Quellung reaction using commercial antisera (SSI Diagnostica; Statens Serum Institut, Copenhagen, Denmark) (15).Serotyping at NML was performed by the Quellung reaction until October 2022; from November 2022 to December 2022, whole-genome sequencing (WGS) was carried out on all isolates submitted to NML using the Illumina platform, with serotypes identified directly using the WGS Analysis and Detection of Molecular Markers (WADE) pipeline, as described  (20,21).Minimum inhibitory concentrations for 2022 isolates were determined using a combination of WGS-predicted susceptibility and in-house broth microdilution (20)(21)(22).Antimicrobials included in this report are penicillin, ceftriaxone, chloramphenicol, clarithromycin, clindamycin, doxycycline, erythromycin, trimethoprim/ sulfamethoxazole, linezolid, and vancomycin.Minimum inhibitory concentration interpretive standards were defined according to CLSI breakpoints (21).Multidrug resistance (MDR) was defined as resistance to three or more classes of antimicrobials for this report.

Data analysis
As previously described (23)

Discussion
The national incidence rate of IPD in Canada for 2021 was 5.6 cases per 100,000 population, which was very similar to 2020 incidence levels (5.9 cases), but far below the incidence in pre-COVID years that ranged from a low of 9.0 cases in 2009 to a high of 10.9 cases in 2018 (Figure 1).The lower rate can be partially attributed to continued COVID-19 non-pharmaceutical intervention strategies (NPIs) instituted in Canada in 2020, such as masking and physical distancing, working and schooling from home, and travel restrictions (24,25).Global studies of pneumococcal disease and co-infection with viruses, such as respiratory syncytial virus (RSV), influenza and metapneumovirus, suggest that decreased incidence of IPD is not only due to NPIs but also associated with decreased circulation of these viruses during COVID-19 lockdown (26-31).A comprehensive interrupted time series study by Rybak et al. that included multiple surveillance systems in France concluded that as pneumococcal carriage rates did not change during periods of NPI use, decreased IPD could be linked to decreased viral infection (29).Gradual lifting of COVID-19 restrictions occurred in Canada in 2022, including a total removal of all travel restrictions in October (24,32).There is concern that a period of increased IPD may occur due to "immunity debt" (lack of stimulation to immune systems) in children, following the lifting of COVID-19related protective measures (27,33,34).Canadian incidence rates for young children aged <1 year and 1 to 4 years jumped from 5.95 to 10.27 and 6.13 to 9.51 cases per 100,000 population, respectively, from 2020 to 2021.An increase was not seen in older age groups (Figure 1).Although incidence rates for IPD are not yet available for 2022, Canada will likely follow the same trend as other countries.The Invasive Respiratory Infection Surveillance (IRIS) Consortium analyzed surveillance data from over thirty countries, including Canada, and reported a worldwide decrease in IPD incidence during the COVID-19 lockdown followed by an increase late in 2021 (35).Increases in the number of IPD isolates received by NML coincided with the lifting of NPIs, particularly in the last quarter of 2022 (Appendix, Figure S1).
PCV13 serotypes 3 and 4 remained the most common serotypes overall for 2021 and 2022.While the prevalence of serotype 3 saw a dip during the 2021 period of NPI strategies in Canada, serotype 4 continued to rise over this same time.This trend can possibly be attributed to the population dynamics and age groups associated with these serotypes.Multiple studies in the western regions of North America show an association of serotype 4 to adults at risk due to homelessness and drug and alcohol abuse (36)(37)(38).Serotype 3 is commonly associated with multiple age groups who would have been more influenced by NPIs than the at-risk populations associated with serotype 4 (39).
Poor immunogenicity of serotype 3 remains an issue; preliminary in vitro immunogenicity studies of the PCV15 vaccine formulation show increased immune response to serotype 3 in comparison to PCV13, but real-world evidence is needed to corroborate these studies (40)(41)(42).
Antimicrobial resistance rates for clarithromycin and erythromycin remained high (both around 24%) but did not trend upward during the study period.Of note is an increase in penicillin resistance (4.7%-8.3%),which can be attributed to an increase in penicillin-resistant serotypes 9V and 19A collected during 2021 and 2022.Over the five-year study period from 2018 to 2022, there was a significant increase in MDR among the isolates  (43).Seventy-one percent of all serotype 9V tested exhibited MDR in 2022 as well as 27% of serotype 23A.This will be crucial to monitor going forward, as a steady increase of common MDR serotypes could have a significant impact on patient outcomes in the future.

Limitations
Caution should be exercised when interpreting the data presented in this report.Provinces and territories may only submit a subset of their isolates to NML for testing.Numbers of isolates submitted to NML versus information submitted to CNDSS may differ due to differences in submission protocols from the provinces.Data for 2020 and 2021 may not be reflective of actual trends, as the COVID-19 pandemic impacted disease incidence in all age groups.Significant increases may have been driven by the large increase in isolates collected in 2022.

Figure
Figure 1: Annual incidence of invasive pneumococcal disease cases per 100,000 population in Canada by age group, 2009-2021 a

Table 1 :
Number of invasive Streptococcus pneumoniae isolates submitted by province, 2021 (18,17)des isolates from Yukon b Includes isolates from New Brunswick, Prince Edward Island, Nova Scotia, and Newfoundland and Labrador c Includes isolates from the Northwest Territories and Nunavut Note: Population-based incidence of disease data for 2009 to 2021 were obtained through the Canadian Notifiable Disease Surveillance System (CNDSS).Population data for incidence rates were obtained from Statistics Canada's annual population estimates elsewhere(16).Isolates that were non-typeable by WGS were confirmed by the Quellung reaction and the National Center for Biotechnology Information (NCBI)'s Basic Local Alignment Search Tool (BLAST) analysis of the rpoB gene(15,17).For this study, serotypes 15B and 15C were grouped together as 15B/C because of reported reversible switching between them in vivo during infection, making it difficult to differentiate between the two types(18,19).Antimicrobial susceptibility testing (AST) was performed on most 2021 IPD isolates submitted to NML for serotyping by the provincial public health laboratories (Saskatchewan, Manitoba, Ontario, Québec, Nova Scotia, Prince Edward Island, Newfoundland and Labrador, and six of eight health regions in New Brunswick).In collaboration with the University of Manitoba and the Canadian Antimicrobial Resistance Alliance, minimum inhibitory concentrations were determined using in-house broth microdilution in accordance with Clinical & Laboratory Standards Institute (CLSI) guidelines

Table 3 )
p<0.0001), however, there was no significant change in the under 15-year age group.Proportions of PCV20-unique and PPV23-unique serotypes have not significantly changed from 2018 to 2022 among the age groups.The number of non-vaccine serotypes overall has decreased from 2018 to 2022 (27.3%-21.5%,p<0.001)(Figure3,Appendix,FiguresS18 to S23 and TablesS2 to S8). .All isolates were susceptible to linezolid and vancomycin.Resistance rates for specific serotypes are listed in Table4and Table5.
(18,mponent of PCV13 b Component of PCV15 c Component of PCV20 d Component of PPV23 e Number of isolates for 2018, 2019, 2020, 2021 and 2022, respectively f For serotypes with an overall (2018-2022) N≥30: up or down arrows indicate statistically significant trends toward increasing or decreasing prevalence for the 2018-2022 timespan, using the chi-squared test for trend.Serotypes with no arrow either did not demonstrate a statistically significant trend, or did not have an overall N≥30 g Serotypes 15B and 15C were grouped together as 15B/C because of reported reversible switching between them in vivo during infection, making it difficult to precisely differentiate between the two types(18,19).Trends for more detailed age groups can be found in the Appendix, Figures S8 to S12

Table 4 :
Percentage of antimicrobial resistance of invasive Streptococcus pneumoniae serotypes collected, 2021

Table 5 :
Percentage of antimicrobial resistance of invasive Streptococcus pneumoniae serotypes collected, 2022 e Serotypes 15B and 15C were grouped together as 15B/C because of reported reversible switching between them in vivo during infection, making it difficult to precisely differentiate between the two types(18,19) f Component of PPV23 CCDR • May 2024 • Vol.50 No. 5 Serotypes 15A and 19A, which have historically exhibited high levels of MDR in Canada, remain a concern; however, similar to the results of the SAVE study described by Adam et al., increased diversity of MDR serotypes was seen

Table S10a :
Prevalence of the ten most common invasive Streptococcus pneumoniae serotypes collected in Western Canada, 2022 Figure S15a: Prevalence of the ten most common invasive Streptococcus pneumoniae serotypes collected in Central Canada, 2021 Figure S15b: Prevalence of the ten most common invasive Streptococcus pneumoniae serotypes collected in Central Canada, 2022 Figure S16a: Prevalence of the ten most common invasive Streptococcus pneumoniae serotypes collected in Eastern Canada, 2021 Figure S16b: Prevalence of the ten most common invasive Streptococcus pneumoniae serotypes collected in Eastern Canada, 2022 Figure S17a: Prevalence of invasive Streptococcus pneumoniae serotypes collected in Northern Canada, 2021 Figure S17b: Prevalence of invasive Streptococcus pneumoniae serotypes collected in Northern Canada, 2022 Figure S18: Proportion of invasive pneumococcal disease isolates by vaccine for the <2-year age group, 2018-2022 Table S2: Proportion of vaccine serotypes for the <2-year age group, 2018-2022 Figure S19: Proportion of invasive pneumococcal disease isolates by vaccine for the 2-4-year age group, 2018-2022 Table S3: Proportion of vaccine serotypes for the 2-4-year age group, 2018-2022 Figure S20: Proportion of invasive pneumococcal disease isolates by vaccine for the 5-14-year age group, 2018-2022 Table S4: Proportion of vaccine serotypes for the 5-14-year age group, 2018-2022 Figure S21: Proportion of invasive pneumococcal disease isolates by vaccine for the 15-49-year age group, 2018-2022 Table S5: Proportion of vaccine serotypes for the 15-49-year age group, 2018-2022 Figure S22: Proportion of invasive pneumococcal disease isolates by vaccine for the 50-64-year age group, 2018-2022 Table S6: Proportion of vaccine serotypes for the 50-64-year age group, 2018-2022 Table S7: Proportion of vaccine serotypes for the ≥65-year age group, 2018-2022 Figure S23: Proportion of invasive pneumococcal disease isolates by vaccine for all age groups, 2018-2022 Table S8: Proportion of vaccine serotypes for all age groups, 2018-2022 Figure S24: Antimicrobial resistance trends of invasive Streptococcus pneumoniae isolates, 2018-2022 Table S9: Multidrug resistance of invasive Streptococcus pneumoniae isolates, 2018-2022 Figure S25a: Invasive Streptococcus pneumoniae serotypes by resistance to different antimicrobial classes, 2021 Figure S25b: Invasive Streptococcus pneumoniae serotypes by resistance to different antimicrobial classes, 2022 Multidrug resistance profiles of invasive Streptococcus pneumoniae serotypes, 2021 Table S10b: Multidrug resistance profiles of invasive Streptococcus pneumoniae serotypes, 2022

Table S11a :
Number of invasive Streptococcus pneumoniae isolates serotyped by the National Microbiology Laboratory (NML) in comparison to the total number of cases reported to Canadian Notifiable Diseases Surveillance System (CNDSS), 2021 List of affiliations 1 National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB 2 Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC