Infection Surveillance Research Articles

Advancing hospital infection surveillance: Automated detection of hospital-onset bacteremia in a large university hospital

Background: Traditional manual surveillance of healthcare-associated infections often neglects certain hospital areas. This study investigated the potential of automated hospital-onset bacteremia (HOB) detection to enhance surveillance comprehensiveness. Our focus was on assessing baseline HOB levels across a large university hospital and demonstrating the algorithm’s ability to discern infection patterns in different hospital areas. Method: Conducted at one of the three sites of Charité university hospital in Berlin, Germany, our study employed an automated HOB detection algorithm, collaboratively developed with the PRAISE (Providing a Roadmap for Automated Infection Surveillance in Europe) network. HOB was defined as a positive blood culture (BC) with a recognized pathogen or two positive BC with common commensals, occurring two days post-admission or later. A retrospective data analysis spanned 2018-2022, with data extraction in January 2024. HOB rates were calculated per 1,000 patient-days and correlated with BC sampling frequency. Trends over time were examined. A comparison was made between intensive care units (ICU) and non-ICU. Result: Data from 58 wards (10 ICU, 48 non-ICU) with 262,058 in-patient admissions and 1,634,793 patient-days were included. Baseline characteristics of the hospital site are summarized in Table 1. Aggregated HOB rates over a 5-year period (Table 2) were substantially higher in ICU compared to non-ICU, applicable to all HOB, HOB with common commensals, and HOB with pathogens. A scatterplot (Figure 1) illustrates a strong correlation between BC sampling frequency and HOB rates in ICU, while Figure 2 displays HOB rates and BC sampling frequency in ICU over time. Notably, HOB rates were higher in the years 2020 and 2021, followed by a decrease in 2022, despite a continually high BC sampling rate. Discussion: The algorithm consistently detected HOB, providing insights into distinctions between ICU and non-ICU. While fewer HOB occurred in non-ICU, continuous monitoring remains crucial, given that the total number of HOB in non-ICU was higher than in ICU, and HOB in non-ICU might currently be overlooked by established surveillance activities. The automated system also demonstrated its effectiveness in identifying trends over time. Although speculative, it appears likely that the higher HOB rates in 2020 and 2021 were at least partially attributable to the COVID-19 pandemic and accompanying factors. There was a notable correlation between HOB and BC sampling frequency. However, the fact that HOB incidence in ICU decreased in 2022 despite persistently high BC sampling frequency rates, indicates the influence of other factors on HOB rates.

A Deeper Look at Proposed Surveillance of Superficial Incision Surgical Site Infections (SSISSIs)

Although the National Healthcare Safety Network (NHSN) recommends the reporting of superficial incisional SSIs, the standardized infection ratio (SIR) models used by the NSHN exclude superficial incisional SSIs cases. Yet, some superficial incisional SSIs may lead to serious adverse patient outcomes. We previously proposed a new category of such infections: serious superficial incisional surgical site infections (SSISSIs), defined as a superficial incisional SSI that (1) required debridement in an operating room and/or (2) led to a hospital readmission within 30 days of surgery. The objective of our study was to determine the prevalence of SSISSIs in a large network of community hospitals and compare hospital rankings of SSI rates of organ/space and deep SSIs (complex SSIs) with and without SSISSIs. We performed a retrospective descriptive analysis of prospectively collected data on 35 NHSN surgical categories in 47 community hospitals within the Duke Infection Control Outreach Network (DICON) from 1/1/2013-12/31/2022. All hospitals used standardized surveillance and data collection strategies throughout the study period. The Wilcoxon rank-sum was used to test for differences in performance rankings of hospitals sorted by rates of complex SSIs alone compared to complex and SSISSI rates. A two-tailed P value of .05 or less was considered significant. Overall, 11,617 SSIs occurred after 1,272,257 surgeries (0.91 SSIs/100 procedures). Out of 3,996 superficial SSIs, 2,038 (17.5% overall, 51.0% of superficial incisional) met criteria for SSISSI. 112 (5.5%) were diagnosed during the current admission and required takeback to the OR for infection; 1,926 (94.5%) were diagnosed during a readmission; and 3841 (33.1%) were diagnosed during readmission and returned to the OR. (Table1) The highest proportion of SSISSIs was diagnosed in patients who underwent gastrointestinal surgery (32.0%) or orthopedic surgery (24.0%). (Table2) Performance ranking of individual hospitals based on rates of complex SSIs, differed significantly when including SSISSIs (p= 0.02). (Table3) Discussion Our findings suggest that SSISSIs make up a moderate but important proportion of SSIs in community hospitals. SSISSIs can be identified through established database surveillance looking at objective measures of returning to the OR for debridement and/or readmission within 30 days. Hospital rankings differed significantly when SSISSIs were added to complex SSIs to calculate SSI rates. As such, including SSISSIs likely provides a more accurate depiction of SSIs with important outcomes and is not as subjective to surveillance bias. Next steps would be specifically to look at outcomes data for complex SSIs compared to SSISSIs to fully evaluate theDisclosure: Jessica Seidelman: UptoDate- Section Editor; BoneSupport- Consultant

Serratia marcescens Burden in a Neonatal Intensive Care Unit: Colonization Rate, Clinical Infections and Strain Relatedness

Background: Serratia marcescens (S. marcescens) is an environmentally associated organism known for causing healthcare associated infections and outbreaks in neonatal intensive care units (NICUs). The colonization or infection rates in NICU settings remain uncertain. This study aims to evaluate the rate of baseline colonization and clinical infection and relatedness of S. marcescens isolates. Methods: Prospective surveillance of rectal colonization and clinical infection of S. marcescens was conducted on patients admitted to the NICU at Mount Sinai Hospital in Toronto, Ontario, from March 1, 2023, to September 30, 2023. The NICU is a 57 bed unit with all private rooms. Monthly point prevalence assessments by rectal screening were performed, alongside active surveillance for clinical infections associated with S. marcesens. Isolates from screening or clinical samples underwent assessment for relatedness using pulse field gel electrophoresis (PFGE). Results: Over the 7 month study period, 12 different patients (5.4%) were colonized/infected with S. marcescens. Among these, 10 patients (4.5%) were identified through rectal screening (316 rectal swabs were collected from 224 patients) and two patients (0.9%) exhibited positive clinical specimens (urine and endotracheal aspirate) in association with pyelonephritis and ventilator-associated pneumonia, respectively. Of the two clinical cases, one case showed a negative preceding rectal swab and the other detected through a clinical sample before the point prevalence date. The age at which a positive S. marcescens swab or positive clinical specimen was identified ranged from 4 to 66 days (median=18 days, IQR 5-38.8) (Figure 1). Sixty seven infants had repeated screening. Three out of 67 (4.5%) were colonized with S. marcescens, the timing and sequence of positive and negative testing are presented in Figure 2. Females demonstrated a higher positivity rate compared to males [9.1% (9/99) vs 2.4% (3/125), p=0.04, respectively]. PFGE analysis of all 12 (100%) isolates revealed a polyclonal pattern. Most cases were detected from March to May in 9/12 cases (75%). Ten different strains were identified. Notably, two strains demonstrated clusters of two cases each, one during March and the other during May (Figure 3). No mortality was reported among the cases. Conclusions: The study highlights the polyclonal nature of S. marcesens and raises questions about the utility of point prevalence in anticipating clinical cases or patient-to-patient transmission, especially in patients with clinical infection where there were no preceding positive screening tests.

Use of proxy indicators for automated surveillance of severe acute respiratory infection, the Netherlands, 2017 to 2023: a proof-of-concept study.

BackgroundEffective pandemic preparedness requires robust severe acute respiratory infection (SARI) surveillance. However, identifying SARI patients based on symptoms is time-consuming. Using the number of reverse transcription (RT)-PCR tests or contact and droplet precaution labels as a proxy for SARI could accurately reflect the epidemiology of patients presenting with SARI.AimWe aimed to compare the number of RT-PCR tests, contact and droplet precaution labels and SARI-related International Classification of Disease (ICD)-10 codes and evaluate their use as surveillance indicators.MethodsPatients from all age groups hospitalised at Leiden University Medical Center between 1 January 2017 up to and including 30 April 2023 were eligible for inclusion. We used a clinical data collection tool to extract data from electronic medical records. For each surveillance indicator, we plotted the absolute count for each week, the incidence proportion per week and the correlation between the three surveillance indicators.ResultsWe included 117,404 hospital admissions. The three surveillance indicators generally followed a similar pattern before and during the COVID-19 pandemic. The correlation was highest between contact and droplet precaution labels and ICD-10 diagnostic codes (Pearson correlation coefficient: 0.84). There was a strong increase in the number of RT-PCR tests after the start of the COVID-19 pandemic.DiscussionAll three surveillance indicators have advantages and disadvantages. ICD-10 diagnostic codes are suitable but are subject to reporting delays. Contact and droplet precaution labels are a feasible option for automated SARI surveillance, since these reflect trends in SARI incidence and may be available real-time.

Alongshan Virus Infection in Rangifer tarandus Reindeer, Northeastern China.

We investigated Alongshan virus infection in reindeer in northeastern China. We found that 4.8% of the animals were viral RNA-positive, 33.3% tested positive for IgG, and 19.1% displayed neutralizing antibodies. These findings suggest reindeer could serve as sentinel animal species for the epidemiologic surveillance of Alongshan virus infection.

Bridging the Gap: Specialized Training Programs for Infection Prevention Specialists Increase Certification Success

Background: The role of the infection preventionist (IP) is complex and encompasses a range of responsibilities requiring extensive knowledge in infection control practices, data analysis, surveillance, performance improvement and collaboration with multidisciplinary teams. Infection prevention certification (CIC) by the certification Board of Infection Control (CBIC) is a standardized marker of knowledge and competencies required for practice in the field. In a 2020 survey of IPs, less than half were certified or planned to become certified. Of those that do take the certification exam, less than three quarters pass on their initial exam attempt. Methods: From 2017 to 2023, fifty-two new IPs were enrolled in a competency-based training program which combined didactic and applied learning on core IP job functions, and a structured mentoring program. The initial didactic phase consisted of evidence-based learning modules with validation of competency through post-training testing and practical demonstration. Education was provided by an advanced practice IP via remote webinars, which included discussion of questions, skills coaching, and review of post-tests. Novice IPs were partnered with at least two preceptors: one advanced practice lead preceptor guided the novice IPs through assigned education modules and oversaw program management and training benchmarks. A second, near-peer preceptor or mentor collaborated with the novice IP in the facility setting. Initial training focused on facility operations, surveillance, rounding and other facility specific activities. Facility mentors were responsible for combining education module topics with practical application of skills. Mentors guided novice IPs through National Healthcare Surveillance network (NHSN) surveillance training and validated surveillance and infection coding until the novice IP had an interrater reliability validation assessing surveillance competency. After the initial training phase, the novice IPs began preparation for certification. This phase included additional training modules aligned with the CBIC certification content outline and practice exams. Results: All 52 novice IPs completed the training program and attempted the CIC examination. The initial pass rate for the certification exam among IPs in the supervised training and mentorship program was 98.1% (n=51). This is 33% higher than the initial pass rate published by CBIC, which was 73.9% (Figure 1). Conclusions: Organizing evidence-based guidelines into topic-specific modules builds a foundation of infection prevention and control knowledge, which is enhanced through remote instruction and direct application of skills under a preceptor’s supervision. This method allows IPs to be introduced to concepts covered in the board certification exam upon hire and support certification with improved outcome

Comparative Analysis of Healthcare-associated Bloodstream Infections & CLABSI Surveillance in A Singaporean tertiary Hospital

Background: Healthcare-associated central line associated bloodstream infection (HA-CLABSI) surveillance is important for monitoring healthcare-associated infections (HAIs) and evaluating effectiveness of infection prevention (IP) measures. However, implementing it is a laborious and time-consuming approach. Exclusive focus on central lines neglects HAI risk due to peripheral vascular catheters. This study aimed to assess whether HA-CLABSI incidence could be inferred from HA-bloodstream infection (BSI) trends and explore shift to HA-BSI surveillance. Methods: The study was performed in a Singaporean tertiary care hospital. Electronic medical records review was performed to determine whether positive blood cultures met Centers for Disease Control/National Health Safety Network (CDC/NHSN) definitions for HA-CLABSI and HA-BSI. Incident episodes of HA-BSI were included (excluding positive cultures repeated within 14 days). Incident organisms were explored to identify common causative pathogens (excluding same organisms isolated from cultures repeated within 14 days). CLABSI and BSI occurring ≥72hrs after admission were considered healthcare-associated. Patients under oncology or hematology service were considered immunocompromised. Incidence rates (IR) per 10,000 patient-days, patient characteristics and causative pathogens were compared between both indicators. Results: From January 2022 to October 2023, mean IR for HA-CLABSI was 0.63 (n=68) and for HA-BSI was 10.06 (n=1094). Median age of patients with HA-CLABSI was 66 years and HA-BSI was 68 years. HA-CLABSI and HA-BSI were more common in males (60.86% & 58.68%). Median duration between admission to HA-CLABSI was 20 days and to HA-BSI was 12 days. Median duration between central line insertion to HA-CLABSI was 16 days. Of 1094, 631 (57.7%) patients had vascular catheter(s) (i.e., IV cannula, port-a-cath, peripherally-inserted central catheter or central line) inserted at time of HA-BSI diagnosis, of whom 46 (7.3%) patients had CLABSI ±2days from positive blood culture. There was no significant correlation between monthly aggregate data from these indicators (Spearman’s correlation coefficient= 0.36, p-value=0.1). Predominant organisms causing HA-CLABSI and HA-BSI were gram negative bacteria (GNB, 40% & 57.21%), gram positive bacteria (24.71% & 22.23%), and fungi. Common GNB in CLABSI patients were Pseudomonas spp. and Stenotrophomonas maltophilia (8.24%), followed by Serratia marcescens and Klebsiella pneumoniae (5.88%). The frequent GNB in HA-BSI patients were Escherichia coli (15.4%), Klebsiella pneumonia (12.68%), and Pseudomonas spp. (6.69%). Common multi-drug resistant organisms were vancomycin-resistant Enterococcus faecium (10.59% & 3.69%) and methicillin-resistant Staphylococcus aureus (10.59% & 3.07%). Conclusion: HA-BSI did not correlate with HA-CLABSI. HA-BSI reflects heterogenous population outcomes. For utilization as surveillance indicator, further assessment on exclusion criteria is required to improve specificity.

Ensuring Accuracy: Making the Case for Inter-rater Reliability in Hospital Acquired Infection Surveillance

Background: Infection preventionists (Ips) have self-reported surveillance as the most time-consuming job task (1,2). APIC’s MegaSurvey 2020 reported that 60% of Ips consider themselves proficient or expert within this competency domain (2). Accurate coding of health care acquired infections is critical to identifying epidemiologically significant events, using data to improve practice, and compliance with state and federal mandated CMS reporting (3,4). Validated case study scenarios were distributed to infection preventionists to better understand how experience level and time spent performing surveillance affects interrater reliability (IRR) in applying the National Healthcare Safety Network (NHSN) surveillance definitions (5,6). Methods: Case study scenarios determined to have high item discrimination were added to an online test bank and distributed annually to Ips of varying experience levels and care settings as part of a mandatory training program (5). The test bank currently consists of forty-two validated questions. Each year, the participants receive approximately thirty questions, including twenty randomly selected from the test bank and ten beta scenarios under development. Only validated test bank scenarios are used to calculate the passing score of 85%. Participants are blinded to which questions are test bank scenarios versus beta scenarios. Additional information was gathered at the beginning of the test to determine CIC status, years of experience, and weekly hours spent doing surveillance. Data was analyzed for passing score on the first attempt for testing years 2019, 2021, 2022, and 2023. Results: Thirty-six Ips passed the IRR test on the first attempt (33%). Of those who passed on the first attempt, twenty-nine (81%) were certified and twenty-two (61%) reported at least nine hours a week performing surveillance. Of the seventy-three Ips (67%) who did not pass on the first attempt, thirty were certified (41%) and sixty (82%) reported performing surveillance for 8 hours or less per week. Conclusion: The first-time pass rate for certified and non-certified Ips was 33%, markedly lower than the self-reported proficiency rate of 60%. The majority of Ips who passed on the first attempt were certified and spent at least nine hours per week performing surveillance. certified and non-certified Ips who did not regularly perform surveillance as part of their weekly job tasks were less likely to pass the test on the first attempt. Given the first-time pass rate among all participants is below optimal, establishing inter-rater reliability systems and ongoing surveillance education for Ips is crucial to ensure accuracy of publicly reported data.

Molecular and Epidemiological Characterization of Pediatric and Adult C. difficile Infection in Canadian Hospitals, 2015-2022

Background: The molecular and epidemiological landscape of C. difficile infection (CDI) has evolved markedly in the last decade; however, limited information is available contrasting differences between adult and pediatric populations. We describe a multicenter study evaluating healthcare-associated (HA) and community-associated (CA) adult and pediatric-CDI identified in the Canadian Nosocomial Infection Surveillance Program (CNISP) network from 2015 to 2022. Methods: Hospitalized patients with CDI were identified from up to 84 hospitals between 2015–2022 using standardized case definitions. Cases were confirmed by PCR, cultured, and further characterized using ribotyping and E-test. We used two-tailed tests for significance (p≤0.05). Results: Of 30,817 cases reported, 29,245 were adult cases [HA-CDI (73.2%), CA-CDI (26.8%)] and 1,572 were pediatric cases [HA-CDI (77.7%), CA-CDI (22.3%)]. From 2015 to 2022, HA-CDI rates decreased 19.7% (p=0.007) and 29.4% (p=0.004) in adult and pediatric populations, respectively (Figure 1). CA-CDI rates remained relatively stable in the adult population (p=0.797), while decreasing 60.7% in the pediatric population (p=0.013). Median ages of adult and pediatric patients were 70 (interquartile range (IQR), 58–80) and seven (IQR, 3–13) years, respectively. Thirty-day all-cause mortality was significantly higher among adult vs. Pediatric CDI patients (11.0% vs 1.4%, p < 0.0001). No significant differences in other severe outcomes were found. Ribotyping and susceptibility data were available for 4,620 samples: 3,558 adult (77.0%) and 1,062 pediatric (23.0%). The predominant adult and pediatric ribotypes (RT) were 106 (12.2/16.2%), 027 (11.4/3.2%), and 014 (8.8/8.2%). Overall, RT027 prevalence significantly decreased from 17.9% in 2015 to 3.2% in 2022 (p=0.003), while RT106 increased from 8.5% to 14.4%. Resistance rates among adult and pediatric isolates were similar for all antimicrobials tested except moxifloxacin (16.2% vs. 6.2%, p < 0.0001, respectively). Adult moxifloxacin resistance decreased from 30% to 6.3% from 2015 to 2022 (p=0.006). Adults with moxifloxacin-resistant CDI were older (median: 74 vs. 69 years, p < 0.001) and had higher thirty-day all-cause mortality (13% vs. 9.8%, p=0.041) and recurrence (10% vs. 5.7%, p < 0.001) compared to those with moxifloxacin non-resistant CDI, while these trends were not observed in pediatric patients. Among RT027 strains, moxifloxacin resistance decreased from 91.0% in 2015 to 7.1% in 2022. There was one metronidazole-resistant pediatric sample in 2018 and no resistance to vancomycin or tigecycline in either population. Conclusion: We have found differences in the epidemiological and molecular characteristics of adult and pediatric CDI, with higher thirty-day all-cause mortality among adults. Overall, RT106 has replaced RT027 as the predominant ribotype with a concomitant decrease in fluoroquinolone resistance.

Burden of Healthcare-Associated Infections in a Pediatric Intensive Care Setting Before, During, and After the Pandemic

Background: Adult rates of non-COVID-19-related healthcare-associated infection (HAI) initially decreased and subsequently increased during the COVID-19 pandemic. Little is known about pediatric HAI rates during this period. Methods: A retrospective review of HAIs was conducted for patients admitted to the intensive care unit (PICU) at a pediatric tertiary care hospital between January 1, 2019 and November 30, 2023. Patients who spent ≥48 hours in the PICU were included. Surgical site infections were excluded. Data were obtained from infection surveillance reports; each HAI was reviewed for validity and attribution based on National Healthcare Safety Network definitions. HAIs were grouped into 3 time periods: pre-pandemic (January 2019-February 2020), pandemic (March 2020- February 2022), and post-pandemic (March 2022-November 2023). Infection rate ratios were calculated for pre-pandemic and post-pandemic periods. Results: Among 2,959 PICU patients admitted during the study period, there were 60 HAI events (4.78 per 1,000 patient days). Rates generally remained steady throughout with slight increases and decreases between time periods (Table 1). There was no significant difference in CAUTI, CLABSI, or HAVRI rates noted in the PICU between pre-pandemic and post-pandemic periods despite a significantly higher device utilization ratio in the post-pandemic period for both urinary catheters and central lines (IRR, 0.89; p < 0 .05; 95% CI, 0.82-0.97). The most frequent HAI in all time periods was CAUTI. Conclusion: Unlike reports from adult centers, no significant variation between time periods was noted for HAIs in our pediatric center. Despite numerous COVID-19-related changes in infection prevention and control measures and contexts throughout the study period, HAI rates remained stable. This may be due in part to the lower burden of critically ill COVID-19 pediatric patients compared to adult populations. Additionally, this could indicate resiliency and consistency in practice among pediatric providers throughout the pandemic. Further evaluation of pediatric HAIs in the context of the COVID-19 pandemic may reveal practices that could be replicated elsewhere to control HAI rates.

National Surgical Site Infection Surveillance System Results Report: July 2021 through June 2022

National Surgical Site Infection Surveillance System Results Report: July 2021 through June 2022

Healthcare-associated infection surveillance automated using artificial intelligence

Healthcare-associated infection surveillance automated using artificial intelligence

Establishing a National Healthcare Associated Infection Surveillance System in Cameroon: Promising Practices and Challenges from Pilot Health Facilities

Establishing a National Healthcare Associated Infection Surveillance System in Cameroon: Promising Practices and Challenges from Pilot Health Facilities

Device and surgical procedure-related infections in Canadian acute care hospitals, 2018-2022.

Healthcare-associated infections (HAIs) are a significant healthcare burden in Canada. National surveillance of HAIs at sentinel acute care hospitals is conducted by the Canadian Nosocomial Infection Surveillance Program. This article describes device and surgical procedure-related HAI epidemiology in Canada from 2018 to 2022. Data were collected from over 60 Canadian sentinel acute care hospitals between January 1, 2018, and December 31, 2022, for central line-associated bloodstream infections (CLABSIs), hip and knee surgical site infections (SSIs), cerebrospinal fluid shunt (CSF) SSIs and paediatric cardiac SSIs. Case counts, rates, patient and hospital characteristics, pathogen distributions and antimicrobial resistance data are presented. Between 2018 and 2022, 2,258 device-related infections and 987 surgical procedure-related infections were reported. A significant rate increase was observed in adult mixed intensive care unit CLABSIs (1.07-1.93 infections per 1,000 line days, p=0.05) and a non-significant rate increase was observed in SSIs following knee arthroplasty (0.31-0.42 infections per 100 surgeries, p=0.45). A fluctuating rate trend was observed in CSF shunt SSIs over the time period and a significant rate decrease in paediatric cardiac SSIs was observed (68%, from 7.5-2.4 infections per 100 surgeries, p=0.01). The most commonly identified pathogens were coagulase-negative staphylococci (22.8%) among CLABSIs and Staphylococcus aureus (42%) among SSIs. Epidemiological and microbiological trends among selected device and surgical procedure-related HAIs are essential for benchmarking infection rates nationally and internationally, identifying any changes in infection rates or antimicrobial resistance patterns and helping inform hospital infection prevention and control and antimicrobial stewardship policies and programs.

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

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

Food and Drinking Water as Sources of Pathogenic Protozoans: An Update

This narrative review was aimed at collecting updated knowledge on the risk factors, illnesses caused, and measures for the prevention of protozoan infections transmitted by food and drinking water. Reports screened dated from 2019 to the present and regarded global prevalence in food handlers, occurrence in food and drinking water, impact on human health, and recently reported outbreaks and cases of severe infections attributable to the dietary route. Cryptosporidium spp., Cyclospora cayetanensis, Entamoeba histolytica, and Cystoisospora belli were the protozoans most frequently involved in recently reported waterborne and foodborne outbreaks and cases. Blastocystis hominis was reported to be the most widespread intestinal protozoan in humans, and two case reports indicated its pathogenic potential. Dientamoeba fragilis, Endolimax nana, and Pentatrichomonas hominis are also frequent but still require further investigation on their ability to cause illness. A progressive improvement in surveillance of protozoan infections and infection sources took place in developed countries where the implementation of reporting systems and the application of molecular diagnostic methods led to an enhanced capacity to identify epidemiological links and improve the prevention of foodborne and waterborne protozoan infections.

Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010-2021.

Carbapenems are last-resort antibiotics for treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance is a rising global threat due to the acquisition of carbapenemase genes. Oxacillinase-48 (bla OXA-48)-type carbapenemases are increasing in abundance in Canada and elsewhere; these genes are frequently found on mobile genetic elements and are associated with specific transposons. This means that alongside clonal dissemination, bla OXA-48-type genes can spread through plasmid-mediated horizontal gene transfer. We applied whole genome sequencing to characterize 249 bla OXA-48-type-producing Enterobacterales isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short- and long-read sequencing, we obtained 70 complete and circular bla OXA-48-type-encoding plasmids. Using MOB-suite, four major plasmids clustered were identified, and we further estimated a plasmid cluster for 91.9 % (147/160) of incomplete bla OXA-48-type-encoding contigs. We identified different patterns of carbapenemase mobilization across Canada, including horizontal transmission of bla OXA-181/IncX3 plasmids (75/249, 30.1 %) and bla OXA-48/IncL/M plasmids (47/249, 18.9 %), and both horizontal transmission and clonal transmission of bla OXA-232 for Klebsiella pneumoniae ST231 on ColE2-type/ColKP3 plasmids (25/249, 10.0 %). Our findings highlight the diversity of OXA-48-type plasmids and indicate that multiple plasmid clusters and clonal transmission have contributed to bla OXA-48-type spread and persistence in Canada.

Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan

Multi-drug resistant (MDR) E. coli constitute a major public health burden globally, reaching the highest prevalence in the global south yet frequently flowing with travellers to other regions. However, our comprehension of the entire genetic diversity of E. coli colonising local populations remains limited. We quantified this diversity, its associated antimicrobial resistance (AMR), and assessed the impact of antibiotic use by recruiting 494 outpatients and 423 community dwellers in the Punjab province, Pakistan. Rectal swab and stool samples were cultured on CLED agar and DNA extracted from plate sweeps was sequenced en masse to capture both the genetic and AMR diversity of E. coli. We assembled 5,247 E. coli genomes from 1,411 samples, displaying marked genetic diversity in gut colonisation. Compared with high income countries, the Punjabi population generally showed a markedly different distribution of genetic lineages and AMR determinants, while use of antibiotics elevated the prevalence of well-known globally circulating MDR clinical strains. These findings implicate that longitudinal multi-regional genomics-based surveillance of both colonisation and infections is a prerequisite for developing mechanistic understanding of the interplay between ecology and evolution in the maintenance and dissemination of (MDR) E. coli.

Profile: The Kenya Multi-Site Serosurveillance (KEMIS) collaboration

The Kenya Multi Site Serosurveillance (KEMIS) collaboration set out to implement an integrated, nationally representative, population-based program of serological surveillance for past infection for a number of important infectious diseases in Kenya. The project started in December 2021 and built on a portfolio of SARS-CoV-2 research conducted in 2020 and 2021. In this profile paper, we describe the background of the KEMIS collaboration, its aim and objectives, the Health and Demographic Surveillance System sites that were involved in data collection, and the key activities undertaken. We also explain how we established governance and management of the KEMIS collaboration, and reflect on opportunities, challenges, lessons learned, and future directions.

Pandemic preparedness improves national-level SARS-CoV-2 infection and mortality data completeness: a cross-country ecologic analysis

BackgroundHeterogeneity in national SARS-CoV-2 infection surveillance capabilities may compromise global enumeration and tracking of COVID-19 cases and deaths and bias analyses of the pandemic’s tolls. Taking account of heterogeneity in data completeness may thus help clarify analyses of the relationship between COVID-19 outcomes and standard preparedness measures.MethodsWe examined country-level associations of pandemic preparedness capacities inventories, from the Global Health Security (GHS) Index and Joint External Evaluation (JEE), on SARS-CoV-2 infection and COVID-19 death data completion rates adjusted for income. Analyses were stratified by 100, 100–300, 300–500, and 500–700 days after the first reported case in each country. We subsequently reevaluated the relationship of pandemic preparedness on SARS-CoV-2 infection and age-standardized COVID-19 death rates adjusted for cross-country differentials in data completeness during the pre-vaccine era.ResultsEvery 10% increase in the GHS Index was associated with a 14.9% (95% confidence interval 8.34–21.8%) increase in SARS-CoV-2 infection completion rate and a 10.6% (5.91–15.4%) increase in the death completion rate during the entire observation period. Disease prevention (infections: β = 1.08 [1.05–1.10], deaths: β = 1.05 [1.04–1.07]), detection (infections: β = 1.04 [1.01–1.06], deaths: β = 1.03 [1.01–1.05]), response (infections: β = 1.06 [1.00–1.13], deaths: β = 1.05 [1.00–1.10]), health system (infections: β = 1.06 [1.03–1.10], deaths: β = 1.05 [1.03–1.07]), and risk environment (infections: β = 1.27 [1.15–1.41], deaths: β = 1.15 [1.08–1.23]) were associated with both data completeness outcomes. Effect sizes of GHS Index on infection completion (Low income: β = 1.18 [1.04–1.34], Lower Middle income: β = 1.41 [1.16–1.71]) and death completion rates (Low income: β = 1.19 [1.09–1.31], Lower Middle income: β = 1.25 [1.10–1.43]) were largest in LMICs. After adjustment for cross-country differences in data completeness, each 10% increase in the GHS Index was associated with a 13.5% (4.80–21.4%) decrease in SARS-CoV-2 infection rate at 100 days and a 9.10 (1.07–16.5%) decrease at 300 days. For age-standardized COVID-19 death rates, each 10% increase in the GHS Index was with a 15.7% (5.19–25.0%) decrease at 100 days and a 10.3% (− 0.00–19.5%) decrease at 300 days.ConclusionsResults support the pre-pandemic hypothesis that countries with greater pandemic preparedness capacities have larger SARS-CoV-2 infection and mortality data completeness rates and lower COVID-19 disease burdens. More high-quality data of COVID-19 impact based on direct measurement are needed.