Healthcare-associated infections and antimicrobial resistance in Canadian hospitals

Abstract

Background: Healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) continue to contribute to excess morbidity and mortality among Canadians.

Objective: This report describes epidemiologic and laboratory characteristics and trends of HAIs and AMR, 2019–2023, 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.

Methods: Data was collected from 109 Canadian sentinel acute care hospitals between January 1, 2019 and December 31, 2023, for Clostridioides difficile infections (CDI), methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSIs), vancomycin-resistant Enterococcus (VRE) BSIs (specifically Enterococcus faecalis and Enterococcus faecium), carbapenemase-producing Enterobacterales (CPE) and carbapenemase-producing Acinetobacter baumannii (CPA) infections and colonizations and Candida auris (C. auris). Trend analysis for case counts, incidence rates (rates), outcomes, molecular characterization and AMR profiles are presented.

Results: Rates remained relatively stable for CDI (range: 4.90–5.35 infections per 10,000 patient days) and MRSA BSI (range: 1.00–1.16 infections per 10,000 patient days) and increased significantly for VRE BSIs (range: 0.30–0.37  infections per 10,000 patient days). Infection rates for CPE remained low compared to other HAIs but doubled non-significantly (rates: 0.08–0.16), CPA counts remained very low (n=4 cases) and C. auris isolates remained low (n=36 isolates).

Conclusion: The incidence of MRSA BSIs and CDI remained stable and VRE BSIs and CPE infections increased in the Canadian acute care hospitals participating in CNISP. Few C. auris isolates were identified. 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.

Introduction

Healthcare-associated infections (HAI) represent one of the most common adverse events experienced by patients in acute care settings globally ^{Footnote 1} . In addition to increasing morbidity and mortality, they are associated with longer lengths of stay in hospitals and higher costs of care ^{Footnote 1} . In Canada, a point prevalence survey conducted in 2017 estimated that the prevalence of patients with at least one HAI was 7.9% ^{Footnote 2} . The prevalence of HAIs between 2015–2018 has been estimated to be at 3.2% in the United States (US), 6.5% in Europe and 9.9% in Australia (and is likely two-fold greater in developing countries) ^{Footnote 1 Footnote 3 Footnote 4 Footnote 5} . In Europe, the cumulative healthcare burden of six HAIs (urinary tract infection, pneumonia, surgical site infection, Clostridioides difficile infections [CDIs], bloodstream infections [BSIs] and neonatal sepsis) was greater than the burden of 32 other communicable diseases combined, including influenza and tuberculosis ^{Footnote 6} . Importantly, a large proportion of HAIs are preventable and evidence from the US showed that advancements in care and infection prevention and control can decrease HAI rates over time ^{Footnote 4} .

Many of the microorganisms that cause HAIs have a propensity for antimicrobial resistance (AMR) and growing rates of resistance threaten to undermine efforts to reduce HAI rates ^{Footnote 6} . Infection with a resistant organism is associated with an 84.4% increased risk of death and in 2019, bacterial AMR was associated with approximately five million deaths globally ^{Footnote 7 Footnote 8} . Canadian data have shown that CDI is associated with a longer length of hospital stay, higher all-cause mortality and an average excess cost of $11,056 per patient ^{Footnote 9} . Other data from Canada and abroad have shown that Staphylococcus aureus (MRSA) BSIs contributed to significant morbidity and mortality, prolonged hospital stays and increased healthcare costs for hospitalized patients ^{Footnote 10 Footnote 11 Footnote 12 Footnote 13} . The rate of AMR is predicted to reach 40% by 2050. In this situation, it is forecasted that 13,700 Canadians could die each year from resistant infections and the overall annual impact to Canada's GDP would be $21 billion ^{Footnote 14} . Moreover, emerging resistant pathogens, such as Candida auris, have necessitated enhanced surveillance and changes to existing infection prevention and control protocols ^{Footnote 15} . Coordinated global public health action, surveillance, improved antibiotic stewardship, infection prevention and control and public awareness are crucial to identify patterns of antimicrobial resistance and prevent and control emerging infections ^{Footnote 16} .

In Canada, the Public Health Agency of Canada (PHAC) collects national data on various HAIs and AMR through the Canadian Nosocomial Infection Surveillance Program (CNISP). Established in 1994, CNISP is a collaboration between the PHAC, the Association of Medical Microbiology and Infectious Disease Canada and sentinel hospitals from across Canada. The goal of CNISP is to facilitate and inform the prevention, control and reduction of HAIs and antimicrobial resistant organisms in Canadian acute care hospitals through active surveillance and reporting.

In line with the World Health Organization's core components of infection prevention and control ^{Footnote 17} , CNISP performs consistent, standardized surveillance to reliably estimate HAI burden, establish benchmark rates for national and international comparison, identify potential risk factors and assess and inform specific interventions to improve patient health outcomes. Data provided by CNISP directly support the collaborative goals outlined in the Pan-Canadian Action Plan on Antimicrobial Resistance ^{Footnote 16} .

In this report, we describe the most recent HAI and AMR surveillance data collected from CNISP participating hospitals between 2019 and 2023.

Methods

Design

The Canadian Nosocomial Infection Surveillance Program conducts prospective, sentinel surveillance for HAIs (including antimicrobial resistant organisms) ^{Footnote 18} .

Case definitions

Standardized case definitions for healthcare-associated (HA) and community-associated (CA) infections were used. Refer to Appendix A for full-case definitions.

Data sources

Between January 1, 2019 and December 31, 2023, participating hospitals submitted epidemiologic data and isolates for cases meeting the respective case definitions for CDIs, MRSA BSIs, vancomycin-resistant Enterococcus (VRE) BSIs (specifically Enterococcus faecalis and Enterococcus faecium) and carbapenemase-producing Enterobacterales (CPE) and carbapenemase-producing Acinetobacter baumannii (CPA) (infections or colonizations). C. auris isolates (infections or colonizations) were identified by provincial and territorial laboratories and participating hospital laboratories. In 2023, 109 hospitals in 10 provinces and one territory participated in HAI surveillance and are further described in Table 1. Hospital participation varied by surveillance project and year (Appendix B, supplemental figures and tables are available upon request from the author). In 2023, CNISP HAI surveillance, patient admissions were categorized according to hospital bed size; small (1–200 beds, n=56 sites, 51%), medium (201–499 beds, n=34 sites, 31%) or large (500 or more beds, n=19 sites, 17%). Hospital participation also varied by region: Western (British Columbia, Alberta, Saskatchewan and Manitoba, n=44 sites, 40%), Central (Ontario and Québec, n=38 sites, 35%), Eastern (Nova Scotia, New Brunswick, Prince Edward Island and Newfoundland and Labrador, n=26 sites, 24%) and Northern (Yukon, Northwest Territories and Nunavut, n=1, 0.9%) (Table 1).

Epidemiologic (demographic, clinical and outcomes) and denominator data (patient days and patient admissions) were collected and submitted by participating hospitals through the Canadian Network for Public Health Intelligence, a secure online data platform.

Reviews of standardized protocols and case definitions are conducted annually by established infectious disease expert working groups; training for data submission is provided to participating CNISP hospital staff as required. Data quality for surveillance projects is periodically evaluated; additional details on the methodology have been published previously ^{Footnote 19 Footnote 20} .

Laboratory data

All patient-linked laboratory isolates (stool samples for CDI cases) were sent to the PHAC's National Microbiology Laboratory for molecular characterization and antimicrobial susceptibility testing. Isolates for MRSA BSIs, VRE BSIs, CPE/CPA (infections or colonizations), C. auris (infections/colonizations) and paediatric CDIs were submitted year-round. Adult CDI isolates were submitted annually during a targeted two-month period (March 1 to April 30).

Statistical analysis

Rates of HAI were calculated by dividing the total number of cases identified in patients admitted to CNISP participating hospitals by the total number of patient admissions (multiplied by 1,000) or patient days (multiplied by 10,000). Due to low case numbers, rates for C. auris were not calculated. The HAI rates are reported nationally and by region. Due to the low number of CA-VRE BSI cases reported each year, stratified rates as well as mortality rates and laboratory results for CA-VRE BSIs were not included in this report. Sites that were unable to provide case data were excluded from rate calculations and missing denominator data were estimated using their previous years reported data, where applicable. Missing epidemiological and molecular data were excluded from analysis. The Mann-Kendall test was used to assess trends in rates over time. The chi-square test for trend was used to analyze trends in proportions over time. The chi-square test was used to compare two categorical variables, while the t-test was used to compare differences between groups. Significance testing was two-tailed and differences were considered significant at p≤0.05. The stability of rates over time indicates that there was no statistically significant trend observed. Where available, all-cause mortality were reported for HAIs. All-cause mortality rate was defined as the number of deaths per 100 HAI cases 30 days following positive culture.

Results

Clostridioides difficile infection

Between 2019 and 2023, overall CDI rates remained stable, ranging from 4.90 to 5.35 infections per 10,000 patient days. Rates initially rose from 2019 to 2020, then decreased from 2020 to 2022, before rising again in 2023. However, no significant trend was observed (p=1.0) (Table 2). The median age among CDI patients was 69 years (IQR: 55–79), with males and females each representing 50% of the total cases (Appendix B).

Source of infection: Stratified by the source of infection, from 2019 to 2023, the incidence of HA-CDI showed little change from 3.62 to 3.56 infections per 10,000 patient days (p=0.31) (Table 2). The CA-CDI rates increased from 1.17 to 1.42 infections per 1,000 patient admissions when comparing 2019 to 2023 rates; however, this trend was not significant (p=0.32) (Table 2).

Regionally, HA-CDI rates have fluctuated across all regions with non-significant changes observed between 2019 and 2023. Specifically, the Western region had an overall decrease from 3.34 to 3.13 infections per 10,000 patient days (p=0.46), the Central region remained stable (3.40–3.77 infections per 10,000 patient days (p=0.61), the Eastern region had a steady rate increase from 2019 to 2021 (2.90–3.58 infections per 10,000 patient days, p=0.09) with a significant drop from 2022 to 2023 (3.58–3.02 infections per 10,000 patient days, p=0.05). For CA-CDI, rates per 1,000 patient admissions remain highest in the Central region from 2019 and 2023 (range: 1.39–1.65), followed by Western (range: 0.99–1.58) and Eastern (range: 0.68–1.05) (Appendix B).

Hospital types: The HA-CDI rates per 10,000 patient days were consistently higher in adult (range: 3.62–3.84, p≤0.005) and paediatric hospitals (range: 3.09–3.61, p≤0.005), with lower rates observed in mixed hospitals (range: 2.57–3.06). The CA-CDI rates per 1,000 patient admissions were higher in adult (range: 1.55–1.77, p≤0.005) and mixed hospital (range: 1.26–1.61), with lower rates observed in paediatric hospitals (range: 0.57–1.15, p≤0.005) between 2019 and 2023 (Appendix B). Stratified by hospital size, rates of HA-CDI were generally highest among large (range: 3.28–3.87), followed by medium (range: 3.15–3.55) and small size hospitals (range: 2.43–2.84). Rates of CA-CDI per 1,000 patient admissions were similar for large (range: 1.23–1.69) and medium sized hospitals (range: 1.22–1.47), and lower for small sized hospitals (range: 0.69–1.19) (Appendix B).

30-day all-cause mortality: Overall 30 day all-cause CDI mortality remained stable over time (range: 8.2–9.0 deaths per 100 cases) (p=0.81) between 2019 and 2023 (Table 2). In 2023, 30-day all-cause mortality was significantly higher for HA-CDI (8.7%) compared to CA-CDI (6.3%) (p=0.02).

Antimicrobial resistance: From 2019 to 2023, 27.1% (n=656/2,424) of CDI isolates were resistant to one or more tested antimicrobials. The proportion of C. difficile isolates resistant to moxifloxacin significantly decreased (p=0.002) between 2019 (11.6%, n=66/568) and 2023 (6.3%, n=32/506) (Table 3). Since 2019, moxifloxacin resistance decreased non-significantly among HA-CDI isolates (5.2%, p=0.22) while a smaller non-significant decrease was observed among CA-CDI (5.4%, p=0.31) (Appendix B). There was no resistance to metronidazole, vancomycin, or tigecycline for all C. difficile isolates tested.

Molecular typing: From 2019 to 2023, the top five most prevalent ribotypes of isolates from HA-CDI defined cases were 106, 014, 020, 002 and 027, with overall prevalences of 15.3%, 9.0%, 6.9%, 6.0% and 5.7%, respectively, while the top five ribotypes of isolates from CA-CDI were 106, 014, 020, 015 and 002, with overall prevalences of 15.2%, 7.9%, 7.4% 5.8% and 5.2%. From 2019 to 2023, the prevalence of RT027 associated with NAP1 decreased from 7.3% to 3.3% and from 3.1% to 2.1%, in HA and CA-CDI populations respectively (Appendix B).

Methicillin-resistant Staphylococcus aureus bloodstream infections

Between 2019 and 2023, overall MRSA BSI rates remained stable, ranging from 1.00 to 1.16 infections per 10,000 patient days. Rates peaked in 2020 (n=1.16) and were lowest in 2022 (n=1.00); however, no significant trend was observed (p=0.462) (Table 4). The median age among MRSA BSI patients was 55 years (IQR: 39–70), with women accounting for 38% of cases (Appendix B).

Source of infection: The CA-MRSA BSI rates increased slightly, from 0.59 in 2019 to 0.67 infections per 10,000 patient days in 2023, though the trend was not significant (p=0.81). Healthcare-associated-MRSA BSI rates remained stable (range: 0.42–0.47 infections per 10,000 patient days) (Table 4).

Regionally, HA-MRSA BSI rates have remained stable across all regions (Western range: 0.47–0.52; Central range: 0.37–0.52; Eastern range: 0.20–0.57; Northern range: 0.00 infections per 10,000 patient days) (Appendix B). The CA-MRSA BSI rates remained stable across all regions except for in the East where there was a significant increase by 0.41 infections per 10,000 patient days (p=0.027) (Western range: 0.70–0.83; Central range: 0.42–0.61; Eastern range: 0.09–0.50; Northern range: 0.00 infections per 10,000 patient days) (Appendix B). In 2023, CA-MRSA BSI rates were highest in Western Canada (0.77 infections per 10,000 patient days), and HA-MRSA BSI rates were highest in Eastern Canada (0.57 infections per 10,000 patient days) (Appendix B).

Hospital types: Both HA- and CA-MRSA BSI rates were consistently higher from 2019 to 2023 in adult (HA-MRSA range: 0.44–0.54, p=0.007; CA-MRSA range: 0.57–0.71, p<0.001) and mixed hospitals (HA-MRSA range: 0.38–0.48, p=0.01; CA-MRSA range: 0.54–0.78, p=0.004), with lower rates observed in paediatric hospitals (HA-MRSA range: 0.24–0.41; CA-MRSA range: 0.28–0.36 infections per 10,000 patient days) (Appendix B). Stratified by hospital size, both HA-and CA-MRSA BSI rates were generally highest among medium (201–499 beds; HA-MRSA p=0.02; CA-MRSA p<0.001) and large size hospitals (500 or more beds; HA-MRSA p=0.07; CA-MRSA p<0.001) (Appendix B).

30-day all-cause mortality: Thirty day all-cause mortality remained stable from 2019 to 2023 (range: 16.4–19.9) (Table 4). In 2023, 30-day all-cause mortality was significantly higher for HA-MRSA (24.7%) compared to CA-MRSA (15.2%) (p<0.001).

Antimicrobial resistance: Clindamycin resistance among MRSA isolates decreased significantly from 40% to 20% between 2019 and 2023 (p=0.027) (Table 5). Since 2019, the proportion of MRSA isolates resistant to erythromycin and ciprofloxacin has stayed relatively stable and high at around 70% in relation to other antibiotics tested. All tested MRSA BSI isolates from 2019 to 2023 were susceptible to linezolid, daptomycin and vancomycin.

Comparing isolates from HA-MRSA with CA-MRSA cases, clindamycin resistance was consistently higher among isolates from HA-MRSA each year from 2019 (47.5%, n=160/337 vs. 30.3%, n=122/403) to 2023 (31.6%, n=87/275 vs. 17.0%, n=70/412) (Appendix B). There were no other notable differences in antibiotic resistance patterns by MRSA BSI case type.

Molecular typing: Between 2019 and 2023, the proportion of spa types identified as t002, most commonly associated with HA-MRSA, continued to decrease from 20.2% of all isolates in HA-MRSA cases in 2019 to 9.5% in 2023 (p<0.001) (Appendix B). Meanwhile, spa type t008, historically most commonly associated with CA-MRSA, continued to increase and account for the largest proportion of isolates identified in CA-MRSA (42.4% in 2019 to 48.8% in 2023, p=0.04) and HA-MRSA defined cases (28.5% in 2019 to 40.0% in 2023, p<0.001) (Appendix B).

Vancomycin-resistant Enterococcus bloodstream infections

From 2019 to 2023, VRE BSI rates significantly increased from 0.30 to 0.37 infections per 10,000 patient days (p=0.02) (Table 6). The median age among patients with VRE BSI was 62 years (IQR: 51–71) and women accounted for 40% of VRE BSI cases (Appendix B).

Source of infection: Vancomycin-resistant Enterococcus BSIs were predominantly HA, as 89.5% (n=1,199/1,339) of VRE BSIs reported from 2019 to 2023 were acquired in a healthcare facility. Stratified by source of infection, HA-VRE BSI rates significantly increased from 2019 to 2023 from 0.27 to 0.33 infections per 10,000 patient days (p=0.03) (Appendix B). CA-VRE BSI rates remained low and stable over time (range: 0.02–0.04 infections per 10,000 patient days).

Regionally, VRE BSI rates in Western Canada significantly increased from 0.29 to 0.48 infections per 10,000 patient days from 2019 to 2023 (p=0.04). No significant trend was observed in Central (range: 0.29–0.39 infections per 10,000 patient days, p=1.00) and Eastern Canada (range: 0–0.04 infections per 10,000 patient days, p=0.16) (Appendix B).

Hospital types: Stratified by hospital type, VRE BSI rates remained highest in adult hospitals from 2019 to 2023 (range: 0.38–0.48 infections per 10,000 patient days). From 2019 to 2023, VRE BSI rates in paediatric hospitals were low (range: 0–0.25 infections per 10,000 patient days). In 2019, VRE BSI rates were highest in small (1–200 beds) and large hospitals (500 or more beds) at 0.35 infections per 10,000 patient days compared to 0.26 infections per 10,000 patient days in medium hospitals (201–499 beds). No significant trend was observed over time across all categories of hospital bed sizes. In 2023, VRE BSI rates in large hospitals were highest at 0.49 infections per 10,000 patient days compared to 0.31 in medium hospitals and 0.16 in small hospitals (Appendix B). The incidence rates for HA-VRE BSI by region, hospital type and hospital size are presented in Appendix B.

30-day all-cause mortality: All-cause mortality remained high and stable over time from 2019 to 2023 (range: 33.5–38.4) (p=0.23) (Table 6).

Antimicrobial resistance: Between 2019 to 2023, high-level gentamicin resistance among VRE BSI isolates (E. faecium) significantly decreased from 32.9% to 18.1% (p=0.01) (Table 6). Daptomycin resistance, significantly decreased from 4.0% (n=7 isolates) in 2019 to 1.8% (n=4 isolates) in 2023 (p=0.04).

Molecular typing: From 2019 to 2023, the majority of VRE BSI isolates were identified as E. faecium; however, one E. faecalis was identified in 2020 (0.7%), 2021 (0.6%) and 2022 (0.5%), respectively, and three (1.4%) in 2023 (Appendix B). The increased presence of VanB among E. faecium changed from 0.6% (n=1) in 2019 to 7.2% (n=16) in 2023 (Appendix B). Among E. faecium isolates, a shift in predominant sequence types was observed over the past five years. The proportion identified as sequence type (ST)1478 was highest in 2019 (31.2%, n=54/173) and significantly decreased to 1.4% (n=3/221) in 2023 (p=0.04) (Appendix B). The proportion of ST17 isolates increased non-significantly from 2019 (17.9% n=31/173) to 2023 (30.3%, n=67/221) (p=0.40) (Appendix B). The proportion of ST80 isolates increased significantly from 2019 (15.6%, n=27/173) to 2023 (31.7%, n=70/221) (p=0.01) (Appendix B) and now represents the predominant ST amongst all tested isolates.

Carbapenemase-producing Enterobacterales (CPE) and Acinetobacter baumannii (CPA)

From 2019 to 2023, CPE infection rates have remained low compared to other HAIs in Canada, although there has been a non-significant increase in the rates over this period (0.08–0.16 infections per 10,000 patient days, p=0.08) (Table 7). The number of CPA infections were very low with five or fewer cases per year between 2019 and 2023. The median age for CPE infections was 65 years and 43% of cases were female (Appendix B).

From 2019 to 2023, the majority of CPE infections (94.8%) were almost equally distributed between Central (49.3%, n=220/446) and Western Canada (45.5%, n=203/446) while few infections were identified in the East (5.2%, n=23/446) (Appendix B). From 2019 to 2023, large hospitals (500 or more beds) generally reported the highest rates of CPE infections (0.09–0.22 infections per 10,000 patient days) compared to small hospitals (fewer than 200 beds) (0.1–0.07 infections per 10,000 patient days. During this period, 30.8% (n=102/331) of CPE-infected patients reported travel outside of Canada and of those, 83.3% (n=75/90) received medical care while abroad. The majority of CPE infections were acquired domestically with 84.2% (n=331/393) of CPE infections acquired in Canada and 81.9% (n=271/331) acquired within a Canadian acute care hospital between 2019 and 2023.

Organisms: Of all isolates submitted (infections and colonizations), the top four carbapenemase producing organisms during 2023 were Escherichia coli (41.3%), Klebsiella pneumoniae (16.4%), Enterobacter cloacae (16.4%) and Citrobacter freundii (14.2%). From 2019 to 2023, there has been an increase in the proportion of E. coli-producing carbapenemases (33%–41.3%) and a decrease in the proportion of K. pneumoniae- (21.4%–16.4%) and E. cloacae- (19.8%–16.4%) producing carbapenemases (Appendix B). The predominant carbapenemases, in order identified in Canada, were K. pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM) and oxacillinase-48 (OXA-48), accounting for 96.2% to 96.0% of identified carbapenemases from 2019 to 2023. Historically, KPC has been the most commonly identified carbapenemase in Canada; however, the proportion of KPC and NDM have been continually trending closer and were almost equal in 2023.

30-day all-cause mortality: All-cause mortality for CPE infections fluctuated between 2019 and 2023 with a mean of 20% (Table 7).

Antibiotic resistance: Multidrug resistance (MDR) and extensive drug resistance (XDR) was observed among CPE (Appendix B) ^{Footnote 21} . In all years, NDM producing isolates were predominantly XDR (range: 83.8–91.8). Conversely, in 2019, OXA-48-like producers were previously associated with a higher proportion of XDR or MDR (89.1%) compared to 2023; (63.5%) showing an overall downward trend in resistance. Klebsiella pneumoniae carbapenemase has been more equally distributed throughout 2019–2023 for either XDR (range: 40.8–50.1) or MDR (range: 40.8–52.2). When examining resistance among the top three carbapenemases, we noted that there was an increase in resistance to all aminoglycosides from 2021 to 2023 in KPC producers (Appendix B). Conversely, among OXA-48-like producers, there was a decline in resistance to aztreonam, doxycycline, levofloxacin, minocycline, trimethoprim/sulfamethoxazole, carbapenems, cephalosporins, tobramycin and gentamicin. This agrees with observations that less OXA-48-like producers were XDR or MDR over time. From 2019 to 2023, the overall resistance in KPC, NDM and OXA-48-like producers to ertapenem was 78.2%, 97.8% and 66.9%, respectively, and for meropenem was 59.1%, 92.3% and 16.5%. respectively. Among new combination drugs, KPC and OXA-48-like producers were highly susceptible to meropenem/vaborbactam and ceftazidime/avibactam. Resistance to imipenem/relebactam by year ranged from 11.1%–17.4% in OXA-48-like producers and 86.3%–93.1% in NDM producers. Meropenem/vaborbactam resistance in NDM producers ranged from 61.3%–76% by year.

Candida auris

Sixty-six percent (n=72/109) of CNISP hospitals participate in C. auris surveillance and between CNISP and the National Microbiology Laboratory surveillance, a total of 36 isolates (colonizations and infections) have been reported from 2019 to 2023. The number of C. auris cases detected per year was seven in 2019, four in 2020, three in 2021, 12 in 2022 and 10 in 2023. Fourteen cases were from Western Canada, 20 cases were from Central Canada and two cases were reported from Eastern Canada. Of the 36 C. auris isolates, 19.4% were resistant to amphotericin B and 77.8% were resistant to fluconazole (Table 8). The amphotericin B resistant isolates were also fluconazole resistant, thus 19.4% of isolates were multidrug-resistant (resistant to two classes of antifungals). Based on available travel information, 73.3% of those reporting travel also received healthcare abroad (Table 8). Of the eleven patients who received healthcare abroad, seven had known carbapenemase-producing organism (CPO) status and two were CPO positive.

Discussion

Canadian Nosocomial Infection Surveillance Program data have shown that between 2019 and 2023, infection rates in Canada have remained relatively stable for CDI (3%) and MRSA BSI (−0.8%). Rates have increased for VRE BSI and CPE infections (23.3% and 100%, respectively), but remain lower than CDI and MRSA BSI rates. A total of 36 C. auris isolates were identified from 2019 to 2023.

The MRSA BSI patients had a median age of 55 years (IQR: 39–70) and were younger compared to those with CDI (69 years) or VRE BSI (62 years) cases. The median time from admission to a positive test for HA-MRSA BSI patients related to your acute care facility was 13 days (IQR: 3–30), which was shorter than for VRE BSI (19 days) and CPE (20 days) but longer than CDI (10 days). The CDI infections occurred more equally between males and females (50% each), compared to 40% females for VRE BSI infections, 38% females for MRSA BSI infections and 43% females for CPE infections (Appendix B).

Trends in CDI rates observed in the CNISP network align with similar trends reported globally ^{Footnote 22} where COVID-19 may have contributed to the increase in 2020 of both HA and CA-CDI rates following pre-COVID-19 pandemic declines ^{Footnote 23} . Beyond COVID-19, HA-CDI rates continued to decline while CA-CDI rates returned to pre-pandemic levels ^{Footnote 23} . When comparing globally, both HA- (3.85 per 10,000 patient days) and CA-CDI (1.83 per 1,000 patient admissions) rates observed in the CNISP network were higher than those reported in acute care hospitals in European Union/European Economic Area countries, which reported an HA-CDI rate of 2.58 per 10,000 patient days and a CA-CDI rate of 1.35 per 1,000 patient admissions in 2020 ^{Footnote 22} .

Clostridioides difficile antimicrobial resistance is less common in Canada than in the US or globally ^{Footnote 24} . In a representative sample of Canadian acute care hospitals, from 2019 to 2023, a 5.3% decrease in moxifloxacin resistance in both HA- and CA-CDI populations is concordant with an overall decrease in the prevalence of RT027. Furthermore, moxifloxacin resistance remained lower (6.3% in 2023) than previously published weighted pooled resistance data for North America (44.0%) and Asia (33.0%) ^{Footnote 25 Footnote 26} . The decline in the prevalence of RT027 has been replaced with a concomitant increase in the prevalence of RT106, RT014 and RT020, consistent with trends observed in the US ^{Footnote 27 Footnote 28} . Additionally, the emergence of RT106 now found worldwide, presents additional challenges as this strain has been shown to produce more spores, have higher rates of recurrence, and is highly resistant to erythromycin, clindamycin, fluoroquinolones and third-generation cephalosporins. The potential emergence of resistant ribotypes warrants further surveillance, monitoring and investigation ^{Footnote 27 Footnote 29} .

Between 2019 and 2023, MRSA BSI rates in the CNISP network remained stable, fluctuating between 1.00 to 1.16 infections per 10,000 patient days. From 2019 to 2023, HA-MRSA BSI rates in CNISP (0.42–0.47 infections per 10,000 patient days), were notably higher than rates reported in Australian public hospitals between 2018 and 2022 (0.11–0.13 infections per 10,000 patient days), likely due to broader CNISP definitions that capture more cases with indirect healthcare links ^{Footnote 30} . However, the CNISP rate for 2023 (0.47 infections) is similar to the rate reported in US hospitals for the same year (0.49 infections per 10,000 patient days), where definitions for laboratory-based surveillance are similar ^{Footnote 31} . The CA-MRSA BSI rate in CNISP for 2023 (0.67 infections per 10,000 patient days) is lower than the rate reported in US hospitals for the same year (0.84 infections), reflective of different populations ^{Footnote 31} . Community-associated-MRSA BSI rates have shown a sustained increase in CNISP data since 2019, suggesting an expanding community reservoir of MRSA in Canada and globally ^{Footnote 32 Footnote 33} .

The CNISP 30-day all-cause mortality rates for MRSA BSI (HA: 20.1%–25.0%; CA: 13.6%–17.4%) were lower than those reported in the US (HA: 29%; CA: 18%) ^{Footnote 33} . Differences may stem from CNISP's strict 30-day mortality cut-off versus undefined US time frames, or from variances in healthcare systems, infection prevention strategies and population characteristics ^{Footnote 34 Footnote 35} .

A significant 20% decrease in clindamycin resistance among MRSA BSI isolates between 2019 and 2023 coincided with shifts in MRSA spa types. The proportion of spa type t002 (commonly HA-MRSA) declined, while spa type t008 (historically CA-MRSA) increased. Notably, t008 rose among CA-MRSA isolates (42.4% to 48.8%) and HA-MRSA isolates (28.5% to 40.0%). This shift underscores the increasing role of CA-MRSA clones in healthcare settings and highlights the dynamic nature of MRSA epidemiology. The growing prevalence of traditionally CA clones in hospitals emphasizes the need for ongoing surveillance and tailored infection prevention strategies. Continued monitoring of antimicrobial resistance patterns is critical for guiding treatment protocols and mitigating MRSA burden in healthcare and community settings. Populations at heightened risk for CA-MRSA infection include children, athletes, incarcerated individuals, seniors with comorbidities and people who inject drugs ^{Footnote 34 Footnote 35}. Injection drug use in particular may signal the emergence of an at-risk population for CA-MRSA. Strategies such as screening and decolonization of MRSA carriers in high-risk populations could help reduce the overall burden of MRSA BSIs ^{Footnote 34 Footnote 35 Footnote 36} .

Vancomycin resistance related to VRE BSI has been shown to be associated with higher mortality rates and longer hospital stays, making it a significant public health concern ^{Footnote 37 Footnote 38 Footnote 39} . Vancomycin-resistant Enterococcus BSI rates observed in the CNISP network increased over time between 2019 and 2023 and were highest in 2023 (0.37 infections per 10,000 patient days). The success of certain sequence types likely contributes to the increased burden of VRE BSI in CNISP-participating hospitals. As of 2023, ST17 (30.3%) and ST80 (31.7%) were the predominant clones overtaking the previously dominant clone ST1478 (1.4%). Compared to other sequence types, a distinct association has been identified between ST80 and the VanB gene. This association of VanB genes harboured predominantly among ST80 isolates has also been documented in recent studies related to VanB outbreaks in Sweden and Denmark ^{Footnote 40 Footnote 41} . The VRE BSI trends are further impacted by the number of high-risk patients admitted to hospital (e.g., bone marrow transplants, solid organ transplants, cancer patients, etc.) ^{Footnote 42 Footnote 43} . Most VRE BSI cases reported by CNISP-participating hospitals were healthcare-acquired, highlighting the importance of appropriate screening, adherence to infection prevention measures and antimicrobial stewardship. Although there is a lack of recent data on VRE BSI rates in comparable jurisdictions, there have been increasing trends noted in Europe ^{Footnote 44 Footnote 45 Footnote 46 Footnote 47 Footnote 48} , which may be associated, in part, with the introduction and spread of new clones and gaps in infection prevention practices ^{Footnote 44 Footnote 45 Footnote 49} .

Carbapenemase-producing Enterobacterales infections are a significant threat to public health as they are becoming increasingly prevalent in healthcare environments worldwide, are associated with high mortality and limited treatment options ^{Footnote 50 Footnote 51 Footnote 52 Footnote 53} . The Centers for Disease Control and Prevention and the World Health Organization have classified CPE as one of the most urgent antimicrobial-resistance threats ^{Footnote 54 Footnote 55} . While the number of CPE infections doubled from 2019 to 2023 in the CNISP network, incidence remained low compared to other HAIs. Data on the incidence of CPE infections in other countries, such as Denmark, Italy, Switzerland and the United Kingdom, have also shown an increasing incidence of CPE infections ^{Footnote 56 Footnote 57 Footnote 58 Footnote 59} . Historically, CPE infections were mostly associated with international travel, but there has been a shift in recent years to domestic acquisition. From 2020 to 2023, 84.6% of CPE infections were domestically acquired and 80.8% were acquired in a Canadian acute care hospital, suggesting that within hospital transmission is driving the recent increase in CPE infection incidence. As a result, strict implementation of infection control measures, including screening in patients with a previous hospital admission domestically and abroad, are useful to reduce the transmission of CPE in Canadian acute care hospitals.

Candida auris is an emerging multidrug resistant fungus that can cause HA invasive infections and outbreaks ^{Footnote 60} . It has been detected across multiple countries and continents including Canada, since its first detection in 2009 ^{Footnote 61 Footnote 62 Footnote 63 Footnote 64} . Candida auris has been associated with outbreaks in healthcare settings in many countries, including Canada and the US, although outbreaks in Canada to date have been limited with few cases ^{Footnote 60} . Reported crude mortality for C. auris ranges widely from 15%–60% but is generally similar to other Candida species ^{Footnote 60 Footnote 61 Footnote 62 Footnote 63 Footnote 64 Footnote 65 Footnote 66} . Though still relatively rare in Canada, the US reported over 4,500 clinical cases and over 9,000 screening cases in 2023 ^{Footnote 67} . The identification of C. auris in routine microbiology laboratories requires identification of Candida to the species level, which may not be routinely performed for isolates from non-sterile sites. Treatment options are limited for patients as approximately one-third of identified C. auris isolates in Canada were multidrug-resistant and additional resistance can develop during antifungal therapy ^{Footnote 68} . Therefore, rapid identification, screening for colonization in at-risk patients and strict implementation of infection prevention and control measures are required to reduce the transmission of C. auris in Canadian healthcare settings. Continued reporting on C. auris in Canada is important to assess and monitor the risk of this pathogen, in addition to identifying epidemiological and microbiological trends ^{Footnote 69} .

Strengths and limitations

The main strength of CNISP is the collection of standardized and detailed epidemiological and laboratory-linked data from 109 sentinel hospitals across Canada for the purpose of providing national HAI and AMR trends for benchmarking and to guide hospital infection prevention and control practices.

Epidemiological data collected by CNISP were limited to information available in-patient charts. Hospital staff turnover may affect the consistent application of CNISP definitions when reviewing medical charts; however, these data were collected by experienced and trained infection prevention and control staff who receive periodic training with respect to CNISP methods and definitions. Furthermore, data quality assessments were conducted to maintain and improve data quality. These data may be subject to potential selection bias due to the exclusion of sites with missing or incomplete data throughout the study period. A limitation of C. auris surveillance is that detailed epidemiologic data are only available on patients identified at CNISP participating hospitals. From 2019 to 2023, CNISP coverage of Canadian acute care beds has increased from 33% to 37%, including increased representativeness in northern, community, rural and Indigenous populations.

Conclusion

Surveillance findings from a national sentinel network of Canadian acute care hospitals indicate that rates of MRSA BSI and CDI have remained stable from 2019 to 2023, while rates of VRE BSI and CPE infections have increased. Few cases of C. auris were detected in Canada. Consistent and standardized surveillance of epidemiologic and laboratory HAI data are essential to providing hospital practitioners with benchmark rates and informing infection prevention and control and antimicrobial stewardship policies to help reduce the burden of HAI and the impact of AMR in Canadian acute care hospitals.

Efforts to improve the quality and representativeness of Canadian HAI surveillance data are ongoing. The enhanced hospital screening practices survey is conducted annually to better understand and contextualize changes in HAI rates in the CNISP network. In addition, CNISP conducts point prevalence survey (PPS) to assess the burden and incidence of HAIs and antimicrobial use in participating Canadian acute care hospitals, and to establish ongoing benchmark rates. CNISP's fourth PPS was conducted from February to March 2024. The CNISP continues to update HAI, antibiotic-resistant organism rates and viral respiratory infection rates, including COVID-19, on a publicly available dashboard using Canada's Health Infobase ^{Footnote 70} . To further improve representativeness and generalizability of national HAI benchmark rates, CNISP has launched a simplified dataset accessible to all acute care hospitals across Canada to collect and visualize annual HAI rate data and has over 100 hospitals participating in the project. Finally, CNISP is exploring HAI surveillance in the long-term care sector in Canada to better understand the burden of HAIs among this at-risk population.

Authors' statement

Canadian Nosocomial Infection Surveillance Program hospitals provided expertise in the development of protocols in addition to the collection and submission of epidemiological data and lab isolates. The National Microbiology Laboratory completed the laboratory analyses and contributed to the interpretation and revision of the paper. Epidemiologists from PHAC were responsible for the conception, analysis, interpretation, drafting and revision of the article.

Competing interests

None.

Acknowledgements

We gratefully acknowledge the contribution of the physicians, epidemiologists, infection control practitioners and laboratory staff at each participating hospital: Vancouver General Hospital (VGH), Vancouver, British Columbia (BC); Richmond General Hospital, Richmond, BC; UBC Hospital, Vancouver, BC; Lion's Gate, North Vancouver, BC; Powell River General Hospital, Powell River, BC; Sechelt Hospital (formerly St. Mary's), Sechelt, BC; Squamish General Hospital, Squamish, BC; Victoria General Hospital, Victoria, BC; Royal Jubilee Hospital, Victoria, BC; Nanaimo Regional General Hospital, Nanaimo, BC; BC Women's Hospital, Vancouver, BC; BC Children's Hospital, Vancouver, BC; Kelowna General Hospital, Kelowna, BC; Penticton Regional Hospital, Penticton, BC; University Hospital of Northern BC, Prince George, BC; Abbotsford Regional Hospital, Abbotsford, BC; Burnaby Hospital, Burnaby, BC; Chilliwack General Hospital, Chilliwack, BC; Delta Hospital, Delta, BC; Eagle Ridge Hospital, Port Moody, BC; Fraser Canyon Hospital, Hope, BC; Langley Memorial Hospital, Langley, BC; Mission Memorial Hospital, Mission, BC; Peace Arch Hospital, White Rock, BC; Royal Columbian Hospital, New Westminster, BC; Ridge Meadows Hospital, Maple Ridge, BC; Surrey Memorial Hospital, Surrey, BC; Queen's Park Centre, New Westminster, BC; Fellburn Care Centre, Burnaby, BC; Fleetwood Place, Surrey, BC; Peter Lougheed Centre, Calgary, Alberta (AB); Rockyview General Hospital, Calgary, AB; South Health Campus, Calgary, AB; Foothills Medical Centre, Calgary, AB; Alberta Children's Hospital, Calgary, AB; University of Alberta Hospital, Edmonton, AB; Stollery Children's Hospital, Edmonton, AB; Royal University Hospital, Saskatoon, Saskatchewan (SK); Regina General Hospital, Regina, SK; Pasqua Hospital, Regina, SK; Moose Jaw Hospital, SK; St. Paul's Hospital, Saskatoon, SK; Health Sciences Centre-Winnipeg, Winnipeg, Manitoba (MB); University of Manitoba Children's Hospital, Winnipeg, MB; Children's Hospital of Western Ontario, London, Ontario (ON); St. Michael's Hospital, Toronto, ON; Victoria Hospital, London, ON; University Hospital, London, ON; Toronto General Hospital, Toronto, ON; Toronto Western Hospital, Toronto, ON; Princess Margaret, Toronto, ON; Mount Sinai Hospital, Toronto, ON; Bridgepoint Active Healthcare, Toronto, ON; Sunnybrook Hospital, Toronto, ON; Kingston General Hospital, Kingston, ON; The Hospital for Sick Children, Toronto, ON; McMaster Children's Hospital, Hamilton, ON; St Joseph's Healthcare, Hamilton, ON; Juravinski Hospital and Cancer Center, Hamilton, ON; Hamilton Health Sciences General Site, Hamilton, ON; The Ottawa Hospital Civic Campus, Ottawa, ON; The Ottawa Hospital General Campus, Ottawa, ON; University of Ottawa Heart Institute, Ottawa, ON; Children's Hospital of Eastern Ontario (CHEO), Ottawa, ON; North York General Hospital, Toronto, ON; Sudbury Regional Hospital, Sudbury, ON; Temiskaming Hospital, Temiskaming Shores, ON; Jewish General Hospital – Sir Mortimer B. Davis (JGH-SMBD), Montréal, Québec (QC); Lachine Hospital, Lachine, QC; Montreal Children's Hospital, Montréal, QC; Hôpital Maisonneuve-Rosemont, Montréal, QC; Hôtel-Dieu de Québec, QC; Centre hospitalier de l'Université de Montréal, Montréal, QC; Montreal General Hospital, Montréal, QC; Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC; Royal Victoria Hospital, Montréal, QC; Montreal Neurological Institute, Montréal, QC; Hôpital régional de Rimouski, Rimouski, QC; Hôpital de Notre-Dame-du-lac, Témiscouata-sur-le-lac, QC; Centre hospitalier régional du Grand-Portage, Rivière-du-loup, QC; Hôpital Notre-Dame-de-Fatima, La Pocatière, QC; Hôpital d'Amqui, Amqui, QC; Hôpital de Matane, Matane, QC; The Moncton Hospital, Moncton, New Brunswick (NB); Halifax Infirmary, Halifax, Nova Scotia (NS); Victoria General, Halifax, NS; Rehabilitation Centre, Halifax, NS; Veterans Memorial Building, Halifax, NS; Dartmouth General Hospital, Halifax, NS; IWK Health Centre, Halifax, NS; General Hospital & Miller Centre, St. John's, Newfoundland and Labrador (NL); Burin Peninsula Health Care Centre, Burin, NL; Carbonear General Hospital, Carbonear, NL; Dr. G.B. Cross Memorial Hospital, Clarenville, NL; Janeway Children's Hospital and Rehabilitation Centre, St. John's, NL; St. Clare's Mercy Hospital, St. John's, NL; Sir Thomas Roddick Hospital, Stephenville, NL; Western Memorial Regional Hospital, Corner Brook, NL; Central Newfoundland Regional Health Centre, Grand Falls-Windsor, NL; James Paton Memorial Hospital, Gander, NL; Dr. Y.K. Jeon Kittiwake Health Centre, New-Wes-Valley, NL; Fogo Island Health Centre, Fogo, NL; Notre Dame Bay Memorial Health Centre, Twillingate, NL; Connaigre Peninsula Health Centre, Harbour Breton, NL; A.M. Guy Health Centre, Buchans, NL; Green Bay Health Centre, Springdale, NL; Baie Verte Peninsula Health Centre, Baie Verte, NL; Queen Elizabeth Hospital, Charlottetown, Prince Edward Island (PE); Prince County Hospital, Summerside, PE; Qikiqtani General Hospital, Nunavut.

Thank you to the staff at Public Health Agency of Canada in the Centre for Communicable Diseases and Infection Control, Ottawa, ON (J Bartoszko, J Cayen, KB Choi, D Lee, C Lybeck, C McClellan, E McGill, R Mitchell, A Neitzel, A-K Nguyen, N Papayiannakis, S Rudat, A Silva, Z Suleman, O Varsaneux) and the National Microbiology Laboratory, Winnipeg, MB (S Ahmed, A Bangit, A Bharat, T Du, R Edirmanasinghe, K Fakharuddin, G Golding, G Grewal, R Hizon, X Li, L Mataseje, M McCracken, M Reimer, N Lerminiaux, J Tinsley).

Funding

This work was supported by Public Health Agency of Canada.

Appendix

Appendix A: Surveillance case definitions and eligibility criteria, 2023

• Clostridioides difficile infection
• Methicillin-resistant Staphylococcus aureus (MRSA) infection
• Vancomycin-resistant Enterococcus (VRE) infection
• Carbapenemase-producing Enterobacterales (CPE) infection
• Candida auris

Appendix B

Supplemental figures and tables are available upon request to the author: cnisp-pcsin@phac-aspc.gc.ca

• Table S1.0: Summary of patient characteristics for Clostridioides difficile infections (CDIs), carbapenemase-producing Enterobacterales (CPE) infections, methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSIs), and vancomycin-resistant Enterococcus (VRE) BSIs, 2019–2023
• Table S1.1: Cases and incidence rates of healthcare-associated and community-associated Clostridioides difficile infection by region, hospital type and hospital size, Canada, 2019–2023
• Table S1.2: Antimicrobial resistance of healthcare-associated and community-associated Clostridioides difficile infection isolates, Canada, 2019–2023
• Table S1.3: Number and proportion of common ribotypes of healthcare-associated and community-associated Clostridioides difficile infection cases, Canada, 2019–2023
• Table S2.1: Cases and incidence rates of healthcare-associated and community-associated methicillin-resistant Staphylococcus aureus bloodstream infections by region, hospital type and hospital size, 2019–2023
• Table S2.2: Antimicrobial resistance of healthcare-associated and community-associated methicillin-resistant Staphylococcus aureus bloodstream infection isolates, Canada, 2019–2023
• Table S2.3: Number and proportion of select methicillin-resistant Staphylococcus aureus spa types (with corresponding epidemic types) identified
• Table S3.1: Number of vancomycin-resistant Enterococcus bloodstream infections incidence rates by region, hospital type and hospital size, 2019–2023
• Table S3.2: Number of healthcare-associated vancomycin-resistant Enterococcus bloodstream infections and incidence rates by region, hospital type and hospital size, 2019–2023
• Table S3.3: Number and proportion of vancomycin-resistant Enterococcus bloodstream infections isolate types identified, 2019–2023
• Table S3.4: Distribution of vancomycin-resistant Enterococcus faecium bloodstream sequence types, 2019–2023
• Table S4.1: Number of carbapenemase-producing Enterobacterales infections and incidence rates by region, hospital type and hospital size, 2019–2023
• Table S4.2: Number and proportion of main carbapenemase-producing pathogens identified
• Table S4.3: Antimicrobial Susceptibility Testing for Klebsiella pneumoniae carbapenemase, 2019–2023
• Table S4.4 Antimicrobial Susceptibility Testing for New Delhi metallo-β-lactamase, 2019–2023
• Table S4.5: Antimicrobial Susceptibility Testing for OXA-48, Oxacillinase-48, 2019–2023

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