Browsing by Author "Conly, John M."
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Item Open Access Antibacterial treatment for exotic species, backyard ruminants and small flocks: a narrative review highlighting barriers to effective and appropriate antimicrobial treatment(2022-06-10) Jelinski, Dana C.; Orsel, Karin; Weese, J. S.; Conly, John M.; Julien, Danielle A.Abstract Antimicrobial resistance is a complex One Health issue that exists in both human and veterinary medicine. To mitigate this ever-growing problem, efforts have been made to develop guidelines for appropriate antimicrobial use (AMU) across sectors. In veterinary medicine, there are notable literature gaps for proper AMU in minor species. We conducted a structured narrative review covering the years of July 2006 – July 2021 to find antimicrobial treatments for common bacterial infections in exotic (birds, rodents, reptiles, and others), small flock (chickens, turkeys, and other fowl), and backyard small ruminant (sheep and goats) species. We retrieved a total of 4728 articles, of which 21 articles met the criteria for our review. Studies were grouped according to species, syndrome, and body system affected. Other data extracted included the bacterial pathogen(s), treatment (active ingredient), and geographical origin. Body systems reported included: intra-oral (n = 4), gastrointestinal (n = 1), respiratory (n = 2), reproductive (n = 1), skin (n = 3), aural (n = 1), ocular (n = 4), and other/multisystem (n = 5). By species, our search resulted in: rabbit (n = 5), rat (n = 2), guinea pig (n = 1), chinchilla (n = 1), guinea pig and chinchilla (n = 1), avian species (n = 1), psittacine birds (n = 2), loris and lorikeets (n = 1), turtles (n = 2), lizards (n = 1), goats (n = 2) and sheep (n = 2). The results of our findings identified a distinct gap in consistent antimicrobial treatment information for commonly encountered bacterial conditions within these species. There is a persisting need for clinical trials that focus on antibacterial treatment to strengthen the evidence base for AMU within exotic, small flock, and backyard small ruminant species.Item Open Access Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta-analysis (November 2019–June 2021)(2022-03-07) Kariyawasam, Ruwandi M.; Julien, Danielle A.; Jelinski, Dana C.; Larose, Samantha L.; Rennert-May, Elissa; Conly, John M.; Dingle, Tanis C.; Chen, Justin Z.; Tyrrell, Gregory J.; Ronksley, Paul E.; Barkema, Herman W.Abstract Background Pneumonia from SARS-CoV-2 is difficult to distinguish from other viral and bacterial etiologies. Broad-spectrum antimicrobials are frequently prescribed to patients hospitalized with COVID-19 which potentially acts as a catalyst for the development of antimicrobial resistance (AMR). Objectives We conducted a systematic review and meta-analysis during the first 18 months of the pandemic to quantify the prevalence and types of resistant co-infecting organisms in patients with COVID-19 and explore differences across hospital and geographic settings. Methods We searched MEDLINE, Embase, Web of Science (BioSIS), and Scopus from November 1, 2019 to May 28, 2021 to identify relevant articles pertaining to resistant co-infections in patients with laboratory confirmed SARS-CoV-2. Patient- and study-level analyses were conducted. We calculated pooled prevalence estimates of co-infection with resistant bacterial or fungal organisms using random effects models. Stratified meta-analysis by hospital and geographic setting was also performed to elucidate any differences. Results Of 1331 articles identified, 38 met inclusion criteria. A total of 1959 unique isolates were identified with 29% (569) resistant organisms identified. Co-infection with resistant bacterial or fungal organisms ranged from 0.2 to 100% among included studies. Pooled prevalence of co-infection with resistant bacterial and fungal organisms was 24% (95% CI 8–40%; n = 25 studies: I2 = 99%) and 0.3% (95% CI 0.1–0.6%; n = 8 studies: I2 = 78%), respectively. Among multi-drug resistant organisms, methicillin-resistant Staphylococcus aureus, carbapenem-resistant Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and multi-drug resistant Candida auris were most commonly reported. Stratified analyses found higher proportions of AMR outside of Europe and in ICU settings, though these results were not statistically significant. Patient-level analysis demonstrated > 50% (n = 58) mortality, whereby all but 6 patients were infected with a resistant organism. Conclusions During the first 18 months of the pandemic, AMR prevalence was high in COVID-19 patients and varied by hospital and geography although there was substantial heterogeneity. Given the variation in patient populations within these studies, clinical settings, practice patterns, and definitions of AMR, further research is warranted to quantify AMR in COVID-19 patients to improve surveillance programs, infection prevention and control practices and antimicrobial stewardship programs globally.Item Open Access Clinical epidemiology and impact of Haemophilus influenzae airway infections in adults with cystic fibrosis(2024-10-27) Weyant, R. Benson; Waddell, Barbara J.; Acosta, Nicole; Izydorczyk, Conrad; Conly, John M.; Church, Deirdre L.; Surette, Michael G.; Rabin, Harvey R.; Thornton, Christina S.; Parkins, Michael D.Abstract Background Haemophilus influenzae is prevalent within the airways of persons with cystic fibrosis (pwCF). H. influenzae is often associated with pulmonary exacerbations (PEx) in pediatric cohorts, but in adults, studies have yielded conflicting reports around the impact(s) on clinical outcomes such as lung function decline. Accordingly, we sought to discern the prevalence, natural history, and clinical impact of H. influenzae in adult pwCF. Methods This single-centre retrospective cohort study reviewed all adult pwCF with H. influenzae sputum cultures between 2002 and 2016. From this cohort, persistently infected subjects (defined as: ≥2 samples with the same pulsotype and > 50% sputum culture-positive for H. influenzae in each year) were matched (1:2) to controls without H. influenzae. Demographic and clinical status (baseline health or during periods of PEx) were obtained at each visit that H. influenzae was cultured. Yearly biobank isolates were typed using pulsed-field gel electrophoresis (PFGE) to assess relatedness. Results Over the study period, 30% (n = 70/240) of pwCF were culture positive for H. influenzae, of which 38 (54%) were culture-positive on multiple occasions and 12 (17%) had persistent infection. One hundred and thirty-seven isolates underwent PFGE, with 94 unique pulsotypes identified. Two (1.5%) were serotype f with the rest non-typeable (98.5%). H. influenzae isolation was associated with an increased risk of PEx (RR = 1.61 [1.14–2.27], p = 0.006), however, this association was lost when we excluded those who irregularly produced sputum (i.e. only during a PEx). Annual lung function decline did not differ across cohorts. Conclusions Isolation of H. influenzae was common amongst adult pwCF but often transient. H. influenzae infection was not associated with acute PEx or chronic lung function decline.Item Open Access A Cost-Effectiveness Analysis of a Decolonization Protocol for Staphylococcus aureus Prior to Hip and Knee Arthroplasty in Alberta, Canada(2019-04-30) Rennert-May, Elissa; Manns, Braden J.; Conly, John M.; Smith, Stephanie Wrenn; Puloski, Shannon K. T.; Henderson, Elizabeth Ann; Loeb, MarkThere are over 100,000 knee/hip replacements yearly in Canada. While these procedures improve mobility and quality of life, approximately 1% develop complex surgical site infections (SSIs) after surgery. Detailed costing analysis of these infections, particularly in Canada, is lacking. We assessed incidence and cost of complex SSIs following primary hip/knee arthroplasty in patients across Alberta. We then evaluated the cost-effectiveness of an evidence-based decolonization protocol in patients prior to hip/knee arthroplasty in Alberta, compared with standard care (no decolonization) using decision analysis. Among 24,667 operations, 1.04% developed a complex SSI. The most common causative pathogen was Staphylococcus aureus (38%). Mean first-year costs for the infected and non-infected cohort were CAN $95,321 (IQR49,623 – 120,636) and $19,893 (IQR12,610 – 19,723), respectively. The decolonization protocol was associated with lower risk of complex SSI and cost savings of $153/person. A decolonization protocol should be considered for implementation in Alberta to reduce infections and save costs.Item Open Access The Cost-Effectiveness of a Prevention Strategy for Clostridioides difficile Infections in Alberta Health Services(2019-04-30) Leal, Jenine Rocha; Manns, Braden; Henderson, Elizabeth Ann; Conly, John M.; Ronksley, Paul Everett; Loeb, Mark; Noseworthy, Tom W.The clinical and economic burden of hospital-acquired Clostridioides difficile infection (HA-CDI) is significant, however there is uncertainty in the cost-effectiveness of implementing probiotics for the primary prevention of HA-CDI among hospitalized patients prescribed antibiotics. In this thesis we examined the predictors of mortality and length of stay among this patient population in Alberta. We determined the attributable cost of HA-CDI and applied these estimates in a cost-effectiveness analysis of probiotics for the primary prevention of HA-CDI in Alberta from the perspective of a publicly-funded healthcare system. We conducted three studies: a population-based, retrospective cohort study using clinical surveillance, administrative and laboratory databases to determine the predictors of 30-day all-cause and attributable mortality and length of stay; a propensity score-matched study to compare patients with HA-CDI to patients without CDI to determine the attributable cost of HA-CDI in Alberta; and a cost-effectiveness analysis using decision analytic modelling to evaluate the costs and consequences related to probiotic use for the primary prevention of CDI. We found that the incidence and mortality rates of HA-CDI are declining, though the latter was not statistically significant. Advancing age was associated with all outcomes after adjusting for a number of baseline factors. Increased baseline white blood cell counts were associated with a lower risk of mortality. Hospital-acquired CDI total adjusted costs were 27% higher and length of stay was 13% higher than non-cases of CDI. Oral probiotics as a preventive strategy for CDI resulted in a lower risk of CDI and cost-savings. Previous studies on the burden of HA-CDI have been limited in their size and scope. Our first study was the largest population-based cohort study evaluating predictors of mortality; while our second study was the first to use propensity score-matching and a micro-costing approach for the estimation of costs associated with HA-CDI. We were the first to conduct an economic evaluation of probiotics for the primary prevention of CDI. This work will be presented to Alberta Health Services to support the evaluation of probiotics as a preventive strategy against CDI and whether to scale up probiotics to all provincial hospitals.Item Open Access Developing an Antimicrobial Stewardship Education Curriculum Framework(2021-03-03) Constantinescu, Cora Mihaela; Kassam, Aliya; Conly, John M.; Vayalumkal, Joseph Varkey; Gilfoyle, ElaineBackground: Antimicrobial Stewardship (AS) education initiatives often neglect to account for the psychosocial factors driving antimicrobial prescribing (AP). Understanding these key factors is important in the design and implementation of tailored educational initiatives. Methods: This study which applied a mixed-methods embedded design, involved quantitative analysis of AS concerns observed by pharmacists through a clinical team rounds audit, as well as qualitative semi-structured interviews based on the Theoretical Domain Framework (TDF). Interviews (n=23) with staff and resident physicians, nurse practitioners and pharmacists were conducted for the Clinical Teaching Unit (CTU) and Pediatric Intensive Care Unit (PICU). We analyzed the data using deductive and inductive methods by mapping nodes from the TDF to a model for social determinants of antimicrobial prescribing (SDAP) in pediatrics. Facilitators and barriers to AP behaviour were identified and represented with respect to Kern’s Model of curriculum development targeted at future PICU and CTU AS education initiatives. Results: The quantitative phase served as an educational needs assessment, identifying chief AS practice (e.g., de-escalation) and antibiotics concerns. The qualitative phase explored AP behaviours and identified psychosocial facilitators and barriers for AS practice. Some facilitators included: 1. Collaboration and trust, 2. Shared decision-making with pharmacy and the Infectious Disease (ID) service, 3. Local accessible guidelines and 4. Overarching goals such as: doing right by the patient and feeling empowered as a prescriber. Some barriers included: 1. The norm of non-interference, 2. Professional comparisons including issues with hierarchy and egos, 3. Limited resources, 4. Feeling inadequately trained in AS, 5. Emotional prescribing in the face of clinical deterioration and diagnostic uncertainty and 6. Pejorative monitoring system. A conceptual framework was then developed using these facilitators and barriers for future educational initiatives for inpatient teams. Conclusions: This study contributes to the gap of knowledge around how best to optimize AS education for multidisciplinary teams. This is the first study in pediatrics taking into consideration the psychosocial drivers of AP behaviour in the context of team decisions around patient-centred clinical rounds. Mapping these facilitators and barriers to an established educational framework, allows for tailored curriculum development of future AS interventions.Item Open Access Health Economic Evaluation of Antimicrobial Stewardship, Procalcitonin Testing, and Rapid Blood Culture Identification in Sepsis Care: A 90-Day Model-Based, Cost-Utility Analysis(2024-11-19) Sligl, Wendy I.; Yan, Charles; Round, Jeff; Wang, Xiaoming; Chen, Justin Z.; Boehm, Cheyanne; Fong, Karen; Crick, Katelynn; Clua, Míriam G.; Codan, Cassidy; Dingle, Tanis C.; Prosser, Connie; Chen, Guanmin; Tse-Chang, Alena; Garros, Daniel; Zygun, David; Opgenorth, Dawn; Conly, John M.; Doig, Christopher J.; Lau, Vincent I.; Bagshaw, Sean M.Abstract Objective We evaluated the cost-effectiveness of a bundled intervention including an antimicrobial stewardship program (ASP), procalcitonin (PCT) testing, and rapid blood culture identification (BCID), compared with pre-implementation standard care in critically ill adult patients with sepsis. Methods We conducted a decision tree model-based cost-effectiveness analysis alongside a previously published pre- and post-implementation quality improvement study. We adopted a public Canadian healthcare payer’s perspective. Two intensive care units in Alberta with 727 adult critically ill patients were included. Our bundled intervention was compared with pre-implementation standard care. We collected healthcare resource use and estimated unit costs in 2022 Canadian dollars (CAD) over a time horizon from study entry to hospital discharge or death. We calculated the incremental net monetary benefit (iNMB) of the intervention group compared with the pre-intervention group. The primary outcome was cost per sepsis case. Secondary outcomes included readmission rates, Clostridioides difficile infections, mortality, and lengths of stay. Uncertainty was investigated using cost-effectiveness acceptability curves, cost-effectiveness plane scatterplots, and sensitivity analyses. Results Mean (standard deviation [SD]) cost per index hospital admission was CAD $83,251 ($107,926) for patients in the intervention group and CAD $87,044 ($104,406) for the pre-intervention group, though the difference ($3,793 [$7,897]) was not statistically significant. Costs were higher in the pre-intervention group for antibiotics, readmissions, and C. difficile infections. The intervention group had a lower mean expected cost; $110,580 ($108,917) compared with pre-intervention ($125,745 [$113,210]), with a difference of $15,165 ($8278). There were no statistically significant differences in quality adjusted life years (QALYs) between groups. The iNMB of the intervention group compared with pre-intervention was greater than $15,000 for willingness-to-pay (WTP) per QALY values of between $0 and $100,000. In our sensitivity analysis, the intervention was most likely to be cost-effective in roughly 56% of simulations at all WTP thresholds. Conclusions Our bundled intervention of ASP, PCT, and BCID among adult critically ill patients with sepsis was potentially cost-effective, but with substantial decision uncertainty.Item Open Access Implementation strategies for hospital-based probiotic administration in a stepped-wedge cluster randomized trial design for preventing hospital-acquired Clostridioides difficile infection(2023-12-11) Bresee, Lauren C.; Lamont, Nicole; Ocampo, Wrechelle; Holroyd-Leduc, Jayna; Sabuda, Deana; Leal, Jenine; Dalton, Bruce; Kaufman, Jaime; Missaghi, Bayan; Kim, Joseph; Larios, Oscar E.; Henderson, Elizabeth; Raman, Maitreyi; Fletcher, Jared R.; Faris, Peter; Kraft, Scott; Shen, Ye; Louie, Thomas; Conly, John M.Abstract Background Clostridioides difficile infection (CDI) is associated with considerable morbidity and mortality in hospitalized patients, especially among older adults. Probiotics have been evaluated to prevent hospital-acquired (HA) CDI in patients who are receiving systemic antibiotics, but the implementation of timely probiotic administration remains a challenge. We evaluated methods for effective probiotic implementation across a large health region as part of a study to assess the real-world effectiveness of a probiotic to prevent HA-CDI (Prevent CDI-55 +). Methods We used a stepped-wedge cluster-randomized controlled trial across four acute-care adult hospitals (n = 2,490 beds) to implement the use of the probiotic Bio-K + ® (Lactobacillus acidophilus CL1285®, L. casei LBC80R® and L. rhamnosus CLR2®; Laval, Quebec, Canada) in patients 55 years and older receiving systemic antimicrobials. The multifaceted probiotic implementation strategy included electronic clinical decision support, local site champions, and both health care provider and patient educational interventions. Focus groups were conducted during study implementation to identify ongoing barriers and facilitators to probiotic implementation, guiding needed adaptations of the implementation strategy. Focus groups were thematically analyzed using the Theoretical Domains Framework and the Consolidated Framework of Implementation Research. Results A total of 340 education sessions with over 1,800 key partners and participants occurred before and during implementation in each of the four hospitals. Site champions were identified for each included hospital, and both electronic clinical decision support and printed educational resources were available to health care providers and patients. A total of 15 individuals participated in 2 focus group and 7 interviews. Key barriers identified from the focus groups resulted in adaptation of the electronic clinical decision support and the addition of nursing education related to probiotic administration. As a result of modifying implementation strategies for identified behaviour change barriers, probiotic adherence rates were from 66.7 to 75.8% at 72 h of starting antibiotic therapy across the four participating acute care hospitals. Conclusions Use of a barrier-targeted multifaceted approach, including electronic clinical decision support, education, focus groups to guide the adaptation of the implementation plan, and local site champions, resulted in a high probiotic adherence rate in the Prevent CDI-55 + study.Item Open Access Longitudinal remotely mentored self-performed lung ultrasound surveillance of paucisymptomatic Covid-19 patients at risk of disease progression(2021-05-30) Kirkpatrick, Andrew W.; McKee, Jessica L.; Conly, John M.Abstract COVID-19 has impacted human life globally and threatens to overwhelm health-care resources. Infection rates are rapidly rising almost everywhere, and new approaches are required to both prevent transmission, but to also monitor and rescue infected and at-risk patients from severe complications. Point-of-care lung ultrasound has received intense attention as a cost-effective technology that can aid early diagnosis, triage, and longitudinal follow-up of lung health. Detecting pleural abnormalities in previously healthy lungs reveal the beginning of lung inflammation eventually requiring mechanical ventilation with sensitivities superior to chest radiographs or oxygen saturation monitoring. Using a paradigm first developed for space-medicine known as Remotely Telementored Self-Performed Ultrasound (RTSPUS), motivated patients with portable smartphone support ultrasound probes can be guided completely remotely by a remote lung imaging expert to longitudinally follow the health of their own lungs. Ultrasound probes can be couriered or even delivered by drone and can be easily sterilized or dedicated to one or a commonly exposed cohort of individuals. Using medical outreach supported by remote vital signs monitoring and lung ultrasound health surveillance would allow clinicians to follow and virtually lay hands upon many at-risk paucisymptomatic patients. Our initial experiences with such patients are presented, and we believe present a paradigm for an evolution in rich home-monitoring of the many patients expected to become infected and who threaten to overwhelm resources if they must all be assessed in person by at-risk care providers.Item Open Access Molecular and genetic determinants associated with the emergence of community-associated methicillin-resistant staphylococcus aureus(2011) Wu, Kaiyu; Zhang, Kunyan; Conly, John M.Item Open Access Patient and ward related risk factors in a multi-ward nosocomial outbreak of COVID-19: Outbreak investigation and matched case–control study(2023-03-22) Leal, Jenine; O’Grady, Heidi M.; Armstrong, Logan; Dixit, Devika; Khawaja, Zoha; Snedeker, Kate; Ellison, Jennifer; Erebor, Joyce; Jamieson, Peter; Weiss, Amanda; Salcedo, Daniel; Roberts, Kimberley; Wiens, Karen; Croxen, Matthew A.; Berenger, Byron M.; Pabbaraju, Kanti; Lin, Yi-Chan; Evans, David; Conly, John M.Abstract Background Risk factors for nosocomial COVID-19 outbreaks continue to evolve. The aim of this study was to investigate a multi-ward nosocomial outbreak of COVID-19 between 1st September and 15th November 2020, occurring in a setting without vaccination for any healthcare workers or patients. Methods Outbreak report and retrospective, matched case–control study using incidence density sampling in three cardiac wards in an 1100-bed tertiary teaching hospital in Calgary, Alberta, Canada. Patients were confirmed/probable COVID-19 cases and contemporaneous control patients without COVID-19. COVID-19 outbreak definitions were based on Public Health guidelines. Clinical and environmental specimens were tested by RT-PCR and as applicable quantitative viral cultures and whole genome sequencing were conducted. Controls were inpatients on the cardiac wards during the study period confirmed to be without COVID-19, matched to outbreak cases by time of symptom onset dates, age within ± 15 years and were admitted in hospital for at least 2 days. Demographics, Braden Score, baseline medications, laboratory measures, co-morbidities, and hospitalization characteristics were collected on cases and controls. Univariate and multivariate conditional logistical regression was used to identify independent risk factors for nosocomial COVID-19. Results The outbreak involved 42 healthcare workers and 39 patients. The strongest independent risk factor for nosocomial COVID-19 (IRR 3.21, 95% CI 1.47–7.02) was exposure in a multi-bedded room. Of 45 strains successfully sequenced, 44 (97.8%) were B.1.128 and differed from the most common circulating community lineages. SARS-CoV-2 positive cultures were detected in 56.7% (34/60) of clinical and environmental specimens. The multidisciplinary outbreak team observed eleven contributing events to transmission during the outbreak. Conclusions Transmission routes of SARS-CoV-2 in hospital outbreaks are complex; however multi-bedded rooms play a significant role in the transmission of SARS-CoV-2.Item Open Access Prolonged SARS-CoV-2 infection following rituximab treatment: clinical course and response to therapeutic interventions correlated with quantitative viral cultures and cycle threshold values(2022-02-05) Thornton, Christina S.; Huntley, Kevin; Berenger, Byron M.; Bristow, Michael; Evans, David H.; Fonseca, Kevin; Franko, Angela; Gillrie, Mark R.; Lin, Yi-Chan; Povitz, Marcus; Shafey, Mona; Conly, John M.; Tremblay, AlainAbstract Background Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is completed through reverse transcriptase-PCR (RT-PCR) from either oropharyngeal or nasopharyngeal swabs, critically important for diagnostics but also from an infection control lens. Recent studies have suggested that COVID-19 patients can demonstrate prolonged viral shedding with immunosuppression as a key risk factor. Case presentation We present a case of an immunocompromised patient with SARS-CoV-2 infection demonstrating prolonged infectious viral shedding for 189 days with virus cultivability and clinical relapse with an identical strain based on whole genome sequencing, requiring a multi-modal therapeutic approach. We correlated clinical parameters, PCR cycle thresholds and viral culture until eventual resolution. Conclusions We successfully demonstrate resolution of viral shedding, administration of COVID-19 vaccination and maintenance of viral clearance. This case highlights implications in the immunosuppressed patient towards infection prevention and control that should consider those with prolonged viral shedding and may require ancillary testing to fully elucidate viral activity. Furthermore, this case raises several stimulating questions around complex COVID-19 patients around the role of steroids, effect of antiviral therapies in absence of B-cells, role for vaccination and the requirement of a multi-modal approach to eventually have successful clearance of the virus.