Background: Healthcare associated infections (HAIs) are a major contributor to patient morbidity and mortality. HAIs are increasingly important due to the rise of multidrug resistant pathogens which can lead to deadly nosocomial outbreaks. Traditional methods for investigating transmissions are slow, costly and have poor detection resolution. In addition, plasmid transmission which can horizontally transfer critical resistance and virulence genes is not part of routine infection control practice due to lack of comprehensive and cost-effective methods capable of identifying both pathogen and/or plasmid transmission. Here we demonstrate the utility of the Oxford Nanopore Technologies (ONT) platform for whole genome sequencing (WGS) based pathogen and plasmids transmission analysis. Methods: We developed a rapid end-to-end process that includes sample preparation, sequencing optimized for generating long-reads and bioinformatics workflow customized for error-prone ONT data. We use Flye to generate de novo assemblies and a secondary bioinformatics step to identify each circular sequence. Individual circular sequences with an Ori (≥1) are identified. For pathogen clonality analysis we perform a pairwise mapping-based chromosomal sequences comparison eliminating need for an external reference genome. Similarly, individual plasmids are separated and compared pairwise. We annotate both the circularized chromosomal and plasmid sequences for known resistance and virulence genes. Results: We performed ONT (and confirmatory Illumina) sequencing of the genomes of 20 bacterial isolates originating from 5 HAI investigations previously performed at Day Zero Diagnostics using epiXact®, our Illumina-based HAI sequencing and analysis lab service. ONT-based clonality determination had 100% agreement with the Illumina based pipeline. We also found that using the outbreak-specific assembled genomes instead of an external reference increased the SNP-calling resolution in the ONT pipeline. We also identified sets of clonal isolates with both identical plasmids and distinct plasmids; as well as sets of non-clonal isolates with identical plasmids and distinct plasmids. In one subset of 7 multi-species isolates, we identified 2-7 circularized plasmid sequences in each isolate, all harboring known resistance genes. 4 plasmids were found in multiple isolates, with each plasmid appearing in between 2 and 4 distinct isolates. Notably, blaNDM was identified in at least 1 plasmid in each isolate. Conclusion: We demonstrate the utility of ONT for comprehensive HAI investigations, establishing the potential to transform healthcare epidemiology with rapid outbreak determination covering pathogen and plasmid transmission in < 2 4 hours from sample receipt.

Background: Bloodstream infections (BSIs) are an important cause of morbidity and mortality in severely ill patients, contributing to increased length of hospital stay and higher cost of care. Alberta Health Services Infection Prevention and Control (IPC) conducts inpatient surveillance of new episodes of BSIs with methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE) or carbapenemase-producing organisms (CPO) in 112 acute care facilities. A case-finding process was undertaken to verify the accuracy of BSI data entry. Methods: All positive MRSA, VRE or CPO blood cultures in 2021 were linked to the Inpatient Discharge Abstract Database (DAD) and the National Ambulatory Care Reporting System (NACRS) to identify new cases during acute care admissions. The results were then compared to surveillance records captured by infection control professionals (ICPs). Cases with unmatched culture date and/or encounter date and cases not identified by ICPs were screened by the study team with final decision made by ICPs. Results were analyzed by ARO and by % increase in number of surveillance records. Results: The laboratory linkage identified 286 new cases. Comparing to surveillance records (n = 248) captured by ICPs, 137 (57.3%) had matching collection dates and encounter dates, 85 (35.6%) had close matches on collection dates and encounter dates, 17 (7.1%) records had either matching collection dates or encounter dates, and 1 (0.4%) record did not have any matches on dates. There were 46 records identified in the laboratory data that were not in the surveillance system and 8 records that were in the surveillance system but not matched to the laboratory data. After review, 22 Surveillance records had data entry errors (1 CPO BSI, 20 MRSA BSI, and 1 VRE BSI), and there were 14 BSI records found to be missing (13 MRSA BSI, 1 VRE BSI). This represents a 6% increase in MRSA BSI and a 3% increase in VRE BSI identified in 2021 and no increase in CPO BSI. Conclusions: A laboratory validation to determine if BSIs with an ARO were missed during routine IPC surveillance identified a small proportion of missed bloodstream infections. The most common reason for the miss was admission through the emergency department with multiple blood cultures collected during a single admission. These results will be shared with the Infection Control program to facilitate correct BSI capture.

Background: Carbapenem-resistant Enterobacterales (CRE) infections are an urgent public health threat. An estimated 12,700 CRE (including E. coli, Klebsiella spp., and Enterobacter spp.) infections occurred in the United States in 2020. While the estimated incidence of CRE infections has been relatively stable between 2012 and 2020, organism-specific trends, including those for organisms not typically included in CRE surveillance definitions, have not been described. We estimated the annual rate of carbapenem-resistant Enterobacterales infections, disaggregated by organism, from 2012 to 2022. Methods: Data on inpatient hospitalizations from a dynamic cohort of short-term acute care hospitals reporting microbiology data between 2012 and 2022 were obtained from the PINC AI Database and the BD Insights Research Database. We included patients with clinical isolates of E. coli, Enterobacter spp., Klebsiella spp., Citrobacter spp., Serratia marcescens, Proteus mirabilis, and Morganella spp. and sufficient susceptibility results to identify carbapenem resistance. We limited our analysis to incident isolates, defined as a patient’s first isolate of a given organism and carbapenem resistance phenotype in a 14-day period. We calculated the annual rate of carbapenem-resistant infections per 10,000 hospitalizations for each organism. Results: There were 3,018,792 incident isolates from 55.8 million hospitalizations included in the analysis. Overall, 31,226 incident carbapenem-resistant isolates were identified. The rate of carbapenem-resistant infections varied by organism and over time (Table 1). The rate of carbapenem-resistant Klebsiella spp. infections appeared to decline from 3.94 in 2012 to 2.44 infections per 10,000 hospitalizations in 2022. The rate of carbapenem-resistant Enterobacter spp. infections appeared to increase from 1.05 in 2012 to 1.44 infections per 10,000 hospitalizations in 2022. The rate of carbapenem-resistant E. coli infections also appeared to increase, from 0.61 in 2012 to 0.85 infections per 10,000 hospitalizations in 2022. Rates of carbapenem-resistant Proteus mirabilis, Morganella spp., Citrobacter spp., or Serratia marcescens infections were similar in 2022 compared to 2012. Conclusions: Disaggregating data by organism revealed heterogeneous trends, with apparent increases in rates of carbapenem-resistant Enterobacter spp. and E. coli infections and apparent decreases in rates of carbapenem-resistant Klebsiella spp. infections. Organism-specific CRE analyses may provide additional insight into CRE epidemiology.

Background: The prevalence of carbapenemase-producing Enterobacteriaceae (CPE) is increasing worldwide. In Canada, where rates of healthcare-associated (HA) transmission of CPE remains relatively low, there is a need to share early experience of universal screening programs and risk factors for HA acquisition. Method: In 2018, universal screening was introduced throughout our large Canadian tertiary care hospital across, all critical care and oncology units. Additionally, risk-factor based screening was applied in all other inpatient units, with further targeted screening of roommate exposures or all inpatients on unit following identification of a single HA case. A retrospective cohort study was carried out on CPE cases detected between January 2018 and December 2023. We assessed the proportion of HA CPE cases, defined as CPE identified in patients with prior admission to our facility or after >72 hours after admission. HA cases were examined for relevant risk factors, including known roommate with CPE, the presence of other CPE on the unit, exposure to outbreak units, prior travel history, travel by a family member, and antibiotic exposure within the past 90 days. Result: A total of 150 CPE cases were identified, with 66 (44%) classified as HA. Among these HA cases, 14 (21%) were associated with presence of known case on the unit. The remaining 52 (79%) represented sporadic nosocomial cases without a known exposure or further transmission on the unit. Upon further retrospective review, 6 (9.2%) HA cases had documented travel history or exposure to a family member with recent travel to China, India, Sri Lanka, or the United States within the past year. Nearly all HA cases (62, 95.4%) had antibiotic exposure within 90 days of CPE detection; specifically, 47 (72.3%) received beta-lactams, 42 (64.6%) cephalosporin, 25 (38.5%) glycopeptide, 20 (30.8%) carbapenem, and 8 (12.3%) macrolide. Conclusion: HA CPE acquisition identified during the first 5-years of universal screening were mostly sporadic and not associated with known exposures or other risk factors. Receipt of prior antibiotics was present in nearly all cases.

Background: In 2018, the Ohio State University College of Veterinary Medicine (OSU CVM) implemented an Antimicrobial Stewardship Program, central to which was the integration of an environmental surveillance (ES) program. The ES focuses on pathogens recognized as urgent threats to public health by the Centers for Disease Control and Prevention. The pathogens currently targeted include carbapenemase-producing Enterobacterales (CPE), Salmonella spp., methicillin-resistant Staphylococcus spp. (MRSs), vancomycin resistant Enterococcus spp., and enrofloxacin resistant Pseudomonas aeruginosa. Identification of these pathogens allows the hospital to be aware of the local environmental microflora which can act as a sentinel for disease in the hospital, potentially causing healthcare associated infections. Therefore, the objective of this program is to identify resistant bacterial pathogens, characterize their resistance profiles, analyze prevalence patterns, and initiate infection control interventions where needed in the OSU VMC. Method: From January 2018 through December 2023, a total of 5449 samples were collected from approximately 86 locations across the OSU VMC encompassing the small animal, equine, and farm animal sections. A majority (64%, n=3561) of samples were collected from the small animal hospital, with the farm animal section contributing 1055 samples and the equine section 899. Areas sampled were frequented by both humans and animals, as well as surfaces exclusively touched by humans. Samples were collected using Swiffers® and processed through selective culture media. Result: Approximately half (52%, n=2890) of the samples collected represented human-touch only surfaces. A total of 3794 bacterial isolates were recovered, with an overall low prevalence for all targeted pathogens. Prevalence of CPE was 2% (n=103), with Enterobacter species being the most common. Recovery of MRSs was 8.5% (n=464) and Salmonella species was 1% (n=47). Conclusion: Through this initiative, the equine division of the OSU VMC collaborated with the antimicrobial stewardship team to enhance their Salmonella fecal and ES practices. In 2019, ES was critical in identifying persistent CPE and extended-spectrum cephalosporin-resistant Enterobacteriaceae in the ICU and surrounding areas of the small animal hospital. Effective measures were taken to halt the spread of ESC among patients and eliminate CPE in the environment. With the discovery of a new CPE in early 2023 in the small animal ICU and nearby areas, the program initiated targeted ES and cleaning and disinfection protocols, to identify contaminated areas and control disease transmission. These efforts have increased patient safety, health, and well-being, demonstrating how ES can be an important tool for infection control and prevention in veterinary settings.

Background: Antimicrobial stewardship programs rely heavily on the electronic medical record (EMR) to carry out daily activities, make interventions, optimize patient care, and collect data. In 2019 the University of Vermont Medical Center transitioned from using a third party platform to the Epic (Verona, WI, www.epic.com) Bugsy module for antimicrobial stewardship. Method: We have spent the past 4 years optimizing the Epic foundation to match our institutional antimicrobial prescribing guidelines, susceptibility patterns, and build reports to extract actionable data. Result: During the build process, we readily identified three areas needed for customization: (1) Empiric, definitive, and prophylactic indications of use for all antimicrobials based on our hospital’s internally published books “Guide to Antimicrobial Therapy for Adults” and “Guide to Antimicrobial Therapy for Pediatrics” (figure 1); (2) An on-demand report to capture all patients with new administrations of antimicrobials in the preceding 72 hours, that includes ordering clinician, stop date of therapy, and indication (figure 2); and (3) A unique, custom-built slicer-dicer report to capture high-level data on how each antimicrobial is being prescribed by indication, dose, route of administration, ordering clinician, attending physician, and department (figure 3). Conclusion: We have built a system where we can readily identify patients that are receiving antimicrobials both within and outside of institutional guidelines and know the ordering clinician to contact to provide in-the-moment feedback. We can also collect retrospective data to know which antimicrobial agents were prescribed for all infectious syndromes. These three institutional customizations have provided invaluable information to improve patient care.

Background: Legionella, first identified in the 1970s, is increasingly recognized as an opportunistic pathogen in healthcare facilities.1 The National University Hospital (NUH) is a large quaternary level academic hospital with 1,200 beds located in equatorial Singapore. Its first building, completed in 1985, still serves patients today. In 2022, the infection prevention team (IPT) was informed of two cases of nosocomial legionella, which sparked the start of an extensive investigation consisting of water quality testing of multiple sources, case finding, and formation of a water management committee. Methods: 250mL water samples were collected and cultured by an external vendor using direct membrane filtration followed by plating on selective agar according to ISO 11731 standards. Bacterial colonies were then identified, quantified and speciated. At the same time, NUH’s facility management measured chlorine levels using a portable colorimeter. Results: In total, we cultured 34 samples taken from sinks, shower heads, potable water dispensers. 91.2% of samples were positive for legionella. Of the 91.2%, 35.3% of sites grew Legionella pneumophila serogroup 1 while 79.4% of sites grew Legionella pneumophila serogroup 2-15. We attributed our high rates of legionella positivity to an aging plumbing system and Singapore’s high humidity and temperatures. In addition, the maximal temperature of our hot water is only 48-50 °C. Although chlorine levels were generally low, they were still within the local recommendation of less than 2ppm (Singapore does not have guidance on minimum chlorine levels). We found no statistically significant correlation between the number of legionella colony forming units (CFUs) and chlorine levels (ranging between 0.02 to 0.14ppm). This supports the United States Environmental Protection Agency’s recommendation, as well as the findings from in vitro and in vivo studies, for a minimal chlorine of 0.2 PPM at the taps for acute care hospitals.2,3However, these levels may be inadequate in the presence of acanthamoeba or a high biofilm load within water systems.4,5 Conclusion: Hospital water management programs should require a minimal level of chlorine at hospital taps and at levels above those recommended by public water systems, in order to control legionella growth. In addition, the formation of a hospital water management committee is essential to improve hospital water quality and put mitigation measures in place. References 1. Phin, N. et al. Epidemiology and clinical management of Legionnaires’ disease. Lancet Infect. Dis. 14, 1011–1021 (2014). 2. Marchesi, I. et al. Monochloramine and chlorine dioxide for controlling Legionella pneumophila contamination: biocide levels and disinfection by-product formation in hospital water networks. J. Water Health11, 738–747 (2013). 3. Cervero-Aragó, S., Rodríguez-Martínez, S., Puertas-Bennasar, A. & Araujo, R. M. Effect of Common Drinking Water Disinfectants, Chlorine and Heat, on Free Legionella and AmoebaeAssociated Legionella. PloS One 10, e0134726 (2015). 4. Kessler, M. A., Osman, F., Marx, J., Pop-Vicas, A. & Safdar, N. Hospital-acquired Legionella pneumonia outbreak at an academic medical center: Lessons learned. Am. J. Infect. Control 49, 1014–1020 (2021).