Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021

Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.

Bloodstream infection and ventilator-associated pneumonia in patients with coronavirus disease 2019 (COVID-19) supported by extracorporeal membrane oxygenation

OBJECTIVE

Extracorporeal membrane oxygenation (ECMO) has been widely used in the care of patients with respiratory failure from coronavirus disease 2019 (COVID-19). We characterized bloodstream infections (BSIs) and ventilator-associated pneumonias (VAPs) in COVID-19 patients supported with ECMO, and we investigated their impact on patient outcomes.

DESIGN

Retrospective cohort study from March 1, 2020, to June 30, 2021.

SETTING

Academic tertiary-care referral center.

PATIENTS

Consecutive adult patients admitted for COVID-19 who received ECMO.

METHODS

We identified BSIs and VAPs and described their epidemiology and microbiology. Cumulative antimicrobial use and the specific management of BSIs were determined. Multivariate time-dependent Cox proportional hazards models were constructed to evaluate the impact of BSIs and VAPs on mortality, controlling for age, receipt of COVID-19-specific therapeutics, and new renal replacement therapy.

RESULTS

We identified 136 patients who received ECMO for COVID-19 pneumonia during the study period. BSIs and VAPs occurred in 81 patients (59.6%) and 93 patients (68.4%), respectively. The incidence of BSIs was 29.5 per 1,000 ECMO days and increased with duration of ECMO cannulation. Enterococci, Enterobacterales, and Staphylococcus aureus were the most common causes of BSIs, whereas S. aureus, Klebsiella species, and Pseudomonas aeruginosa comprised the majority of VAPs. Mean antibiotic use comprised 1,031 days of therapy per 1,000 ECMO days (SD, 496). We did not detect an association between BSIs or VAPs and mortality.

CONCLUSIONS

BSIs and VAPs are common in COVID-19 ECMO-supported patients. Efforts to optimize their diagnosis, prevention, and management should be prioritized.

Trends in Clostridioides difficile infection rates in Canadian hospitals during the coronavirus disease 2019 (COVID-19) pandemic

The coronavirus disease 2019 (COVID-19) pandemic has placed significant burden on healthcare systems. We compared Clostridioides difficile infection (CDI) epidemiology before and during the pandemic across 71 hospitals participating in the Canadian Nosocomial Infection Surveillance Program. Using an interrupted time series analysis, we showed that CDI rates significantly increased during the COVID-19 pandemic.

Gut microbiome modified by bariatric surgery improves insulin sensitivity and correlates with increased brown fat activity and energy expenditure

Alterations in the microbiome correlate with improved metabolism in patients following bariatric surgery. While fecal microbiota transplantation (FMT) from obese patients into germ-free (GF) mice has suggested a significant role of the gut microbiome in metabolic improvements following bariatric surgery, causality remains to be confirmed. Here, we perform paired FMT from the same obese patients (BMI > 40; four patients), pre- and 1 or 6 months post-Roux-en-Y gastric bypass (RYGB) surgery, into Western diet-fed GF mice. Mice colonized by FMT from patients' post-surgery stool exhibit significant changes in microbiota composition and metabolomic profiles and, most importantly, improved insulin sensitivity compared with pre-RYGB FMT mice. Mechanistically, mice harboring the post-RYGB microbiome show increased brown fat mass and activity and exhibit increased energy expenditure. Moreover, improvements in immune homeostasis within the white adipose tissue are also observed. Altogether, these findings point to a direct role for the gut microbiome in mediating improved metabolic health post-RYGB surgery.

Effect of faecal microbial transplant via colonoscopy in patients with severe obesity and insulin resistance: A randomized double-blind, placebo-controlled Phase 2 trial

AIM

To assess the effects of faecal microbial transplant (FMT) from lean people to subjects with obesity via colonoscopy.

MATERIAL AND METHODS

In a double-blind, randomized controlled trial, subjects with a body mass index ≥ 35 kg/m² and insulin resistance were randomized, in a 1:1 ratio in blocks of four, to either allogenic (from healthy lean donor; n = 15) or autologous FMT (their own stool; n = 13) delivered in the caecum and were followed for 3 months. The main outcome was homeostatic model assessment of insulin resistance (HOMA-IR) and secondary outcomes were glycated haemoglobin levels, lipid profile, weight, gut hormones, endotoxin, appetite measures, intestinal microbiome (IM), metagenome, serum/faecal metabolites, quality of life, anxiety and depression scores.

RESULTS

In the allogenic versus autologous groups, HOMA-IR and clinical variables did not change significantly, but IM and metabolites changed favourably (P < 0.05): at 1 month, Coprococcus, Bifidobacterium, Bacteroides and Roseburia increased, and Streptococcus decreased; at 3 months, Bacteroides and Blautia increased. Several species also changed significantly. For metabolites, at 1 month, serum kynurenine decreased and faecal indole acetic acid and butenylcarnitine increased, while at 3 months, serum isoleucine, leucine, decenoylcarnitine and faecal phenylacetic acid decreased. Metagenomic pathway representations and network analyses assessing relationships with clinical variables, metabolites and IM were significantly enhanced in the allogenic versus autologous groups. LDL and appetite measures improved in the allogenic (P < 0.05) but not in the autologous group.

CONCLUSIONS

Overall, in those with obeisty, allogenic FMT via colonoscopy induced favourable changes in IM, metabolites, pathway representations and networks even though other metabolic variables did not change. LDL and appetite variables may also benefit.

Epidemiology of primary and recurrent healthcare-associated and community-associated pediatric Clostridioides difficile infection in Canada, 2015-2020

Clostridioides difficile infection (CDI) among children remains a concerning cause of morbidity in hospital settings. We present epidemiological and molecular trends in healthcare- and community-associated CDI among children in Canadian inpatient and outpatient settings, including those who experienced recurrent infections.

1524. SARS-CoV-2 Infection Incidence Following Exposure Assessments for Healthcare Workers

Background

Although healthcare worker (HCW) absenteeism due to COVID-19 exposure represents a significant challenge, there are currently no evidence-based criteria for assessing infection risk based on COVID-19 exposure type. We aimed to identify the incidence of acquiring infection following varying exposures to COVID-19 to guide safe return-to-work policies for staff in healthcare settings.

Methods

We analyzed prospectively collected data at an academic centre with approximately 17 000 active staff between January 1 - April 30, 2022 during a large BA.1 Omicron surge. More than 99% of staff received >2 vaccine doses. All staff self-reporting household, community, and workplace exposure to confirmed cases of COVID-19 submitted attestation to the Occupational Health department detailing the nature of the exposure, the duration, and setting. Staff were required to report all positive test results by rapid antigen or PCR testing.

Results

A total of 3209 staff submitted exposure reports (2493 household, 539 community, and 177 workplace). Of these, 1008 (31.4%) tested positive 2 days prior to or 14 days after the exposure (36% household; 19% community, 7% workplace). In the community exposure group, 19% tested positive due to a discrete exposure of < 4 hours and 21% tested positive with an exposure >4 hours. For household exposures and workplace exposures, these values were 25%/27% and 6%/10%, respectively (Figure 1). The median time to testing positive was 2 days for household exposures and 3 days for community and workplace exposures (Figure 2, Panels A-C). By day 4 post-exposure, more than 80% of positive results were reported (Figure 2, Panel D). Risk of testing positive differed based on baseline symptom status at the time of reporting (Table 1).

Risk of infection during the peri-exposure period (2 days before reported exposure and 14 days after) according to type and duration of exposure. Background rate of infection based on regional incidence of disease due to BA.1 Omicron wave.

SARS-CoV-2 Infection Risk (A - household; B - Community; C - Workplace) after exposure. Time to infection in all groups is shown in panel D.

The risk of infection amongst healthcare workers reporting exposures, according to their symptom status at the time of reporting their exposures.

Conclusion

Our data suggests that the highest risk of acquiring SARS-CoV-2 was via household contacts, regardless of exposure duration, with workplace exposures carrying less risk. Using a cut-off of 4 hours for exposure duration to delineate risk may be of limited value. These data could help workplaces predict infection risk following exposure and guide return-to-work policies that balance the need to staff workplaces, including hospitals, with reducing risk of on-site transmission during periods of increased community transmission (Figure 3).

Risk of Infection in the Context of Background Infection

Background general population infection risk based on regional incidence of disease due to BA.1 Omicron wave.

Disclosures

All Authors: No reported disclosures.

Characterization of Healthcare-Associated and Community-Associated Clostridioides difficile Infections among Adults, Canada, 2015-2019

We investigated epidemiologic and molecular characteristics of healthcare-associated (HA) and community-associated (CA) Clostridioides difficile infection (CDI) among adult patients in Canadian Nosocomial Infection Surveillance Program hospitals during 2015–2019. The study encompassed 18,455 CDI cases, 13,735 (74.4%) HA and 4,720 (25.6%) CA. During 2015–2019, HA CDI rates decreased by 23.8%, whereas CA decreased by 18.8%. HA CDI was significantly associated with increased 30-day all-cause mortality as compared with CA CDI (p<0.01). Of 2,506 isolates analyzed, the most common ribotypes (RTs) were RT027, RT106, RT014, and RT020. RT027 was more often associated with CDI-attributable death than was non-RT027, regardless of acquisition type. Overall resistance C. difficile rates were similar for all drugs tested except moxifloxacin. Adult HA and CA CDI rates have declined, coinciding with changes in prevalence of RT027 and RT106. Infection prevention and control and continued national surveillance are integral to clarifying CDI epidemiology, investigation, and control.

422. Sustainability of Improvements to Hand Hygiene Performance Throughout the COVID-19 Pandemic

Background

Hand hygiene (HH) is a standard infection prevention and control precaution to be applied in healthcare settings to prevent transmission of COVID-19. Many healthcare institutions observed significant improvements in HH performance during wave one of the COVID-19 pandemic but the sustainability of this change is unknown. Our aim was to evaluate long-term HH performance throughout subsequent waves of the pandemic across acute care hospitals in Ontario, Canada.

Methods

HH adherence was measured using a previously validated group electronic monitoring system which was installed on all alcohol handrub and sink soap dispensers inside and outside each patient room across 56 inpatient units (35 wards and 21 critical care units) spanning 13 acute care hospitals (6 university and 7 community teaching hospitals) from 1 November 2019 to 31 May 2021. Daily HH adherence was compared with daily COVID-19 case count across Ontario. During this period, weekly performance continued to be reported to units but unit-based quality improvement discussions were inconsistent due to the COVID-19 response.

Results

Figure 1 depicts daily aggregate HH adherence plotted against the new daily COVID-19 case count across Ontario. An elevation in HH adherence was seen prior to the start of the first wave, rising almost to 80% and then remained above 70% for the peak of wave one. During waves two and three, peak COVID-19 case counts were associated with a maximum HH adherence of 51%, only marginally above the pre-pandemic baseline. After the end of wave one (from 1 July 2020 to 31 May 2021) the median HH performance was only 49% (interquartile range 47%-50%).

Figure 1. Hand hygiene adherence across 13 acute care hospitals in comparison to overall new daily COVID-19 cases in Ontario

Conclusion

Initial improvements in HH adherence preceding the start of the COVID-19 pandemic were not sustained, possibly due to increasing comfort and reduced anxiety associated with providing care to COVID-19 patients leading to a perception of reduced COVID-19 transmission risk. These findings highlight the need for HH monitoring to be tied to longitudinal unit-led quality improvement in order to achieve durable changes in practice.

Disclosures

Susy S. Hota, MSc MD FRCPC, Finch Therapeutics (Research Grant or Support) Susy S. Hota, MSc MD FRCPC, Finch Therapeutics (Individual(s) Involved: Self): Grant/Research Support

Out of sight, out of mind: a prospective observational study to estimate the duration of the Hawthorne effect on hand hygiene events

Background

Human auditing has been the gold standard for evaluating hand hygiene (HH) compliance but is subject to the Hawthorne effect (HE), the change in subjects’ behaviour due to their awareness of being observed. For the first time, we used electronic HH monitoring to characterise the duration of the HE on HH events after human auditors have left the ward.

Methods

Observations were prospectively conducted on two transplant wards at a tertiary centre between May 2018 and January 2019. HH events were measured using the electronic GOJO Smartlink Activity Monitoring System located throughout the ward. Non-covert human auditing was conducted in 1-hour intervals at random locations on both wards on varying days of the week. Two adjusted negative binomial regression models were fit in order to estimate an overall auditor effect and a graded auditor effect.

Results

In total, 365 674 HH dispensing events were observed out of a possible 911 791 opportunities. In the adjusted model, the presence of an auditor increased electronic HH events by approximately 2.5-fold in the room closest to where the auditor was standing (9.86 events per hour/3.98 events per hour; p<0.01), an effect sustained across only the partial hour before and after the auditor was present but not beyond the first hour after the auditor left. This effect persisted but was attenuated in areas distal from the auditor (total ward events of 6.91*6.32–7.55, p<0.01). Additionally, there was significant variability in the magnitude of the HE based on temporal and geographic distribution of audits.

Conclusion

The HE on HH events appears to last for a limited time on inpatient wards and is highly dynamic across time and auditor location. These findings further challenge the validity and value of human auditing and support the need for alternative and complementary monitoring methods.

Challenges establishing a multi-purpose fecal microbiota transplantation stool donor program in Toronto, Canada

BACKGROUND

The success of fecal microbiota transplantation (FMT) programs depends on maintaining suitable stool donors. We describe challenges recruiting and retaining universal donors in the first 2 years of an FMT clinical and research program in Toronto and identify opportunities for improvement.

METHODS

A four-stage screening process is used to identify suitable FMT donors in the Microbiota Therapeutics Outcomes Program. Donor screening follows Health Canada recommendations and excludes persons with history or risk for diseases associated with dysbiosis. Donors are rescreened microbiologically approximately every 1-3 months and answer ongoing health, exposure, and dietary questionnaires.

RESULTS

In the first 2 years of our program, 5 of 322 (1.6%) prospective stool donors passed initial screening, and only 2 (0.6%) were retained. Most prospective donors were excluded on telephone screening, at which point high BMI, medication use, and family history of relevant illness were common exclusions. No candidate was excluded because of a concerning physical examination. Microbiologic reasons for donor exclusion included carriage of Blastocystis hominis (n = 2), Helicobacter pylori (n = 2), extended spectrum beta-lactamase producing organisms (n = 1), Shiga-toxin producing Escherichia coli (n = 1), and sapovirus (n = 1). Universal donors were lost temporarily because of travel, antibiotic exposures, and transient carriage of antibiotic-resistant organisms.

CONCLUSIONS

Recruiting and retaining suitable donors for FMT is challenging because of rigorous exclusions and labour-intensive screening processes. We present considerations for efficiency in donor screening, including targeting recruitment populations, expanded website self-screening, eliminating physical examinations, and streamlining post-travel risk assessment.

Sink-Related Outbreaks and Mitigation Strategies in Healthcare Facilities

PURPOSE OF REVIEW

In this review, we summarize recent outbreaks attributed to hospital sinks and examine design features and behaviors that contributed to these outbreaks. The effectiveness of various risk mitigation strategies is presented. Finally, we examine investigational strategies targeted at reducing the risk of sink-related infections.

RECENT FINDINGS

Outbreaks of hospital sink-related infections involve a diverse spectrum of microorganisms. They can be attributed to defects in sink design and hospital wastewater systems that promote the formation and dispersion of biofilm, as well as healthcare practitioner and patient behaviors. Risk mitigation strategies are often bundled; while they may reduce clinical cases, sink colonization may persist. Novel approaches targeting biofilms show promise but require more investigation. Emphasis should be placed on optimizing best practices in sink design and placement to prevent infections. Hospitals should consider developing a rational surveillance and prevention strategy based on the current design and state of their sinks.

Regional variability in fecal microbiota transplantation practices: a survey of the Southern Ontario Fecal Microbiota Transplantation Movement

BACKGROUND

There is growing evidence that fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection, but little guidance exists for implementation of FMT programs. The objective of this study is to describe the program characteristics and protocols of 9 planned or operating FMT programs in the Southern Ontario Fecal Microbiota Transplantation (SOFT) Movement, to help guide future FMT program implementation.

METHODS

A 59-item survey was administered electronically to clinical leads of the SOFT Movement on June 2, 2016. The survey evaluated 7 domains: FMT program characteristics, FMT recipients, donor screening/selection, transplant manufacturing, FMT administration, good manufacturing procedures/biosafety procedures and infection-control procedures. We used descriptive statistics to analyze quantitative data.

RESULTS

All 9 programs responded to the survey: 6 were active, 1 had FMT standard operating procedures developed but did not have clinical experience, and 2 were in the process of forming FMT programs. All 6 active programs performed FMT in adult patients with C. difficile infection. About 1300 FMT procedures were performed between 2003 and 2016. Five of the 6 operating programs administered the preparation via enema. Programs were driven primarily by physicians. All programs used universal FMT donors and followed Health Canada's screening guidelines, with considerable variability in screening frequency (every 3-6 mo) and modality. Locations for transplant preparation and manufacturing protocols varied across programs. Stool mass for FMT ranged from 20 g to 150 g, and transplant volume ranged from 25 mL to 300 mL.

INTERPRETATION

The experience of this high-volume regional FMT network highlights current challenges in FMT program development, including a high reliance on physicians and the costly nature of donor screening. Standardization and optimization through development of regional centres of excellence for FMT donor recruitment and administration should be explored.

Is a Single Fecal Microbiota Transplant a Promising Treatment for Recurrent Clostridium difficile Infection?

Clostridium difficile infection, a common hospital-associated infection, is a gastrointestinal illness that becomes recurrent in about 25% of infected patients. Fecal microbiota transplantation (FMT) is increasingly supported by clinical trials as an effective treatment for recurrent Clostridium difficile infection, but a number of questions remain about how it can be optimally performed. In this Perspective, we discuss controversies in FMT methodologies and reporting within randomized controlled trials, all of which may influence clinical outcomes in treated patients. Finally, we focus on the question of whether single vs multiple FMTs are necessary to achieve favorable outcomes for the treatment of recurrent Clostridium difficile infection, postulating on why there may be an association between number of FMTs and clinical effectiveness.

Oral Vancomycin Followed by Fecal Transplantation Versus Tapering Oral Vancomycin Treatment for Recurrent Clostridium difficile Infection: An Open-Label, Randomized Controlled Trial

Background

Fecal transplantation (FT) is a promising treatment for recurrent Clostridium difficile infection (CDI), but its true effectiveness remains unknown. We compared 14 days of oral vancomycin followed by a single FT by enema with oral vancomycin taper (standard of care) in adult patients experiencing acute recurrence of CDI.

Methods

In a phase 2/3, single-center, open-label trial, participants from Ontario, Canada, experiencing recurrence of CDI were randomly assigned in a 1:1 ratio to 14 days of oral vancomycin treatment followed by a single 500-mL FT by enema, or a 6-week taper of oral vancomycin. Patients with significant immunocompromise, history of fulminant CDI, or irreversible bleeding disorders were excluded. The primary endpoint was CDI recurrence within 120 days. Microbiota analysis was performed on fecal filtrate from donors and stool samples from FT recipients, as available.

Results

The study was terminated at the interim analysis after randomizing 30 patients. Nine of 16 (56.2%) patients who received FT and 5 of 12 (41.7%) in the vancomycin taper group experienced recurrence of CDI, corresponding with symptom resolution in 43.8% and 58.3%, respectively. Fecal microbiota analysis of 3 successful FT recipients demonstrated increased diversity. A futility analysis did not support continuing the study. Adverse events were similar in both groups and uncommon.

Conclusions

In patients experiencing an acute episode of recurrent CDI, a single FT by enema was not significantly different from oral vancomycin taper in reducing recurrent CDI. Further research is needed to explore optimal donor selection, FT preparation, route, timing, and number of administrations.

Clinical Trials Registration

NCT01226992.

Decay and Fission Hindrance of Two- and Four-Quasiparticle K Isomers in ^{254}Rf

Two isomers decaying by electromagnetic transitions with half-lives of 4.7(1.1) and 247(73) μs have been discovered in the heavy ^{254}Rf nucleus. The observation of the shorter-lived isomer was made possible by a novel application of a digital data acquisition system. The isomers were interpreted as the K^{π}=8^{-}, ν^{2}(7/2^{+}[624],9/2^{-}[734]) two-quasineutron and the K^{π}=16^{+}, 8^{-}ν^{2}(7/2^{+}[624],9/2^{-}[734])⊗8^{-}π^{2}(7/2^{-}[514],9/2^{+}[624]) four-quasiparticle configurations, respectively. Surprisingly, the lifetime of the two-quasiparticle isomer is more than 4 orders of magnitude shorter than what has been observed for analogous isomers in the lighter N=150 isotones. The four-quasiparticle isomer is longer lived than the ^{254}Rf ground state that decays exclusively by spontaneous fission with a half-life of 23.2(1.1) μs. The absence of sizable fission branches from either of the isomers implies unprecedented fission hindrance relative to the ground state.

Determining mortality rates attributable to Clostridium difficile infection

To determine accuracy of measures of deaths attributable to Clostridium difficile infection, we compared 3 measures for 2007–2008 in Ontario, Canada: death certificate; death within 30 days of infection; and panel review. Data on death within 30 days were more feasible than panel review and more accurate than death certificate data.

Surgical treatment for incessant pericarditis

A case of chronic relapsing pericarditis is presented in which all forms of medical therapy failed. Pericardectomy was performed as a last resort, with complete resolution of symptoms. Incessant pericarditis, as distinguished from recurrent intermittent pericarditis, may respond favourably to surgical removal, especially in the presence of recurrent pericardial effusion.