bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coinfections in hospitalized COVID-19 patients are associated with high mortality: need for improved diagnostic tools
Authors: Kothadia Sonya , Wilson Brigid , Perez Federico , Bonomo Robert 
Published: May 2022

Background: Hospitalized patients with COVID-19 often receive antimicrobial therapies due to concerns for bacterial and fungal coinfections. We analyzed patients admitted with COVID-19 to our VA facility to understand antimicrobial use, frequency of coinfections, and outcomes in our population. Methods: This retrospective study included veterans who were 18 years or older and hospitalized with COVID-19 from March 10, 2020, to March 9, 2021 at the Louis Stokes VA Medical Center in Cleveland, Ohio. We identified antimicrobials administered and coinfections with bacterial or fungal pathogens. Patients were deemed to have coinfection if there was supporting microbiological data and a consistent clinical course upon review of clinical records. Urinary tract infections were excluded because of difficulty determining infection. Odds ratios (ORs) and 95% confidence intervals (CIs) for 30-day mortality were derived using multivariate logistic regression models that included age, Charlson comorbidity index (CCI), corticosteroid use, and time of infection. Results: In our cohort of 312 patients, the median age was 70 years and 97% of the patients were male. The mean CCI was 3.7 (SD, 3.0), and 111 patients (35.6%) had a score ≥5. Oxygen was administered to 250 patients (80.1%), and 20 (6.4%) required mechanical ventilation. Antimicrobials were administered to 164 patients (52.6%) (Fig. 1). Of 20 patients (6.4%) with coinfection, 11 (3.5%) had a bloodstream infection (BSI) and 9 (2.9%) had bacterial pneumonia (Fig. 2). The overall 30-day mortality rate was 12.5% (39 of 312). Among patients with coinfection, the 30-day mortality rate was 45% (9 of 20). Diagnoses of BSI (OR, 6.35; 95% CI, 1.41–26.30) and bacterial pneumonia (OR, 9.34; 95% CI, 2.01–46.34) were associated with increased mortality. Of the data available, 12 (63%) of 19 patients with coinfection had elevated procalcitonin levels (ie, >0.50). At the time of COVID-19 diagnosis, the median absolute lymphocyte count in patients who died was 0.7 K/mm3 (95% CI, 0.6–1.12) in comparison to 1 K/mm3 (95% CI, 0.7–1.4) in patients who survived at 30 days. Conclusions: Our analysis of hospitalized COVID-19 patients with advanced age and underlying comorbid conditions demonstrated that coinfections were infrequent but that they were independently associated with increased mortality. This finding highlights the need for better tools to diagnose the presence or absence of bacterial and fungal coinfection in COVID-19 patients. Our findings also emphasize the need for judicious use of antimicrobials while discerning which patients are at risk of critical illness and mortality.Funding: NoneDisclosures: None
Work system factors affecting COVID-19 PPE use: A human factors approach to analysis of video recordings of emergency department clinical work
Authors: Nosakhare Esosa , Perry Shawna , Peterson Susan , Catalfumo Frankie , Osei Kelly , Osei Kelly , Osei Kelly , Williams Kelly , Bradley Maia , Sultan Marium , Daodu Oluseyi , Prabhu Nivedha , Gurses Ayse 
Published: May 2022

Background: The effectiveness of PPE in preventing self-contamination of healthcare workers (HCWs) and transmission of pathogens (airborne and contact) in the emergency department (ED) is highly dependent on consistent, appropriate use of and other interactions (eg, storing, cleaning, etc) with the PPE. Pre–COVID-19 studies focused primarily on individual HCW contributions to incorrect or suboptimal PPE use. We conducted an analysis of ED video recordings using a human-factors engineering framework (ie, The Systems Engineering Initiative for Patient Safety, SEIPS), to identify work-system–level contributions to inappropriate PPE usage by HCWs while they provide care in their actual clinical care environment. Methods: In total, 47 video sessions (each ~15 minute) were recorded between June 2020 and May 2021 using a GoPro camera in an 8-bed pod area, designated for persons under investigation (PUI) and confirmed COVID-19–positive patients, in an ED of a large, tertiary-care, academic medical center. These recordings captured a ‘landscape view’: 2 video cameras were set up to capture the entire ED pod area and HCWs as they provided care. A team with hemorrhagic fever expertise, infection prevention and control expertise, and ED expertise reviewed each video together and extracted data using a semistructured form. Results: Guided by the 5 components of the SEIPS work system model, (ie, task, physical environment, person, organization, tools and technology), multiple work system failure points influencing HCWs appropriate use of PPE were identified. For example, under the task component, HCWs were observed not doffing and donning in recommended sequence. Also, inconsistencies with COVID-19 status signage on a patient’s door and ambiguous labelling of work areas designated as clean (donning) and dirty (doffing) sites acted as a barrier to appropriate PPE use under the physical environment section. Conclusions: Human factors–based analysis of video recordings of actual ED work identified a variety of work system factors that impede appropriate or correct use of PPE by HCWs. Future efforts to improve appropriate PPE use should focus on eliminating or mitigating the effects of these work system factors.Funding: US CDCDisclosures: The authors gratefully acknowledge the CDC for funding this work. This material is based upon work supported by the Naval Sea Systems Command (under contract No. N00024-13-D-6400, Task Order NH076). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the Naval Sea Systems Command (NAVSEA) or the US CDC.
Prioritizing SARS-CoV-2 testing in a highly immunosuppressed patient population
Authors: Shackelford Jenna , Woolbert Michele , Sinaii Ninet , Decker Brooke , Palmore Tara , Odom Robin T 
Published: May 2022

Background: The NIH Clinical Center implemented multiple testing protocols to facilitate early detection and isolation of SARS-CoV-2 infected patients and rooming-in family members (RIFMs). Beginning in February 2020, all symptomatic patients were tested; in March 2020, all patients were tested prior to aerosol-generating procedures (AGPs); and in May 2020, all patients and RIFMs were tested on admission. We sought to determine the value of SARS-CoV-2 testing practices in our hospital. Methods: Respiratory specimens collected March 2020 through June 2021 tested for SARS-CoV-2 by RT-PCR were reviewed, and corresponding patient clinical and demographic variables were collected. Repeated tests from SARS-CoV-2–positive persons were excluded from the data. Results associated with multiple testing indications were assigned the highest priority reason based on a predetermined hierarchy. Data were analyzed using the χ2 test and logistic regression. Results: Of 12,706 results from 5,704 patients, primary testing reasons were pre-AGP (n = 5,387, 43.0%), admission (n = 2,733; 21.8%), and symptomatic testing (n = 2,701; 21.6%). Overall, 159 tests (1.25%) were positive for SARS-CoV-2. Asymptomatic patients tested on admission were 1.8 times more likely to be positive than outpatients tested for any reason (P = .003) and 4.2 times more likely than asymptomatic inpatients tested prior to AGP (P = .003). Within asymptomatic pre-AGP testing, there was no difference between inpatients (0.46%) and outpatients (0.65%). Hispanic patients were 1.9 times more likely to be positive. (p Conclusions: At a hospital with a geographically broad referral base, admissions COVID-19 testing was far more fruitful than pre-AGP testing of inpatients. Pre-AGP used the most testing resources yet had the lowest yield. Admissions testing remains beneficial regardless of community transmission rates, while testing prior to AGP could be pared back when community rates of COVID-19 are low and redeployed when community rates rise. Conclusions: Our findings that Hispanic persons had higher risk and that transplant patients had lower risk of testing positive suggests differences in the extent to which each subgroup may have been able to shelter from COVID-19 in the community during this earlier phase of the pandemic. Keeping immunocompromised patients safe from COVID-19 while they undergo longitudinal care involves layered precautions in the hospital and in the community that must evolve in response to evidence and epidemiological trends.Funding: NoneDisclosures: None
Is your ice machine really clean? Uncovering the presence of opportunistic pathogens in hospital ice machines
Authors: Cazals Margot , Bedard Emilie , Prévost Michèle , Savard Patrice 
Published: May 2022

Background: Ice is used in healthcare facilities for medical purposes and consumption by the medical staff and the patients, but some studies have revealed significant microbial contamination of ice machines leading to nosocomial outbreaks or pseudooutbreaks and infections by opportunistic pathogens, including the fungi Candida, the bacteria Pseudomonas aeruginosa, and nontuberculous mycobacteria (NTM). Although ice machines are complex devices that are prone to contamination, very little is known about their potential as vectors of infections for populations at risk in hospitals. Only few studies document efficient maintenance regimes, specifically cleaning procedures and microbial indicators that would ensure their safe use. Method: In this prospective study, combined samples of water and ice, and drain biofilm samples were collected from 36 ice and cold-water distribution machines of a recently built hospital, for a total of 72 samples. Physicochemical parameters (total and free chlorine, temperature, etc) were measured in water, and several opportunistic pathogens (ie, Candida spp, P. aeruginosa, NTM) and biological indicators (ie, heterotrophic plate counts (HPCs), total and viable bacteria and enterococci) were monitored in water and ice and biofilm. Culture methods were used for HPCs, Candida spp, P. aeruginosa, and enterococci, and total and viable bacterial populations were estimated using flow cytometry. NTM were monitored by quantitative polymerase chain reaction (qPCR). Results: We observed clear differences between the machines in terms of biological contamination, with frequent detection of NTM and presumed Candida. Thus, NTM were detected in the 36 samples of ice and water with concentrations from 0.5 to 2×104 gene copies/mL. Among the several species of fungi detected in the ice machines, some were identified as C. parapsilosis and C. guilliermondii, which are organisms of concern in healthcare facilities. Factors affecting the level of contamination in ice machines include the location of the machines and water quality (ie, temperature and chlorine residual concentration). Depending on the location in the building and the model of ice machine sampled, the biological indicators measurements indicated more or less significant contamination. No link was established between environmental strains recovered from the machines and clinical infections. Conclusions: Monitoring results showed that ice machines, while subject to few regulations and controls, can be reservoirs of unsuspected opportunistic pathogens that could lead to nosocomial infections of vulnerable patients. Cleaning procedures should be based on the disinfection of resistant opportunistic pathogens, such as Candida and NTM, and the use of general indicators, such as HPCs, should be questioned.Funding: NoneDisclosures: None
Susceptibility reporting and antibiotic prescribing for UTIs in the inpatient setting: A nudge toward improved stewardship
Authors: Ponder Madison , Kinlaw Alan , Daniels Lindsay , Norris Ashlyn , Alby Kevin 
Published: May 2022

Background: Urinary tract infections (UTIs) are common in the inpatient, observation, and emergency department settings. Although many UTI-causing pathogens are susceptible to oral β-lactams, these agents are not tested directly, and susceptibility is extrapolated from other agents. To improve the use of these agents, the University of North Carolina Medical Center (UNCMC) added cephalexin to the susceptibility profile generated with urine culture results in the electronic health record (EHR). We evaluated prescribing trends of cephalexin, other oral β-lactams, fluoroquinolones, and other antibiotics for UTIs in the inpatient setting, before and after the susceptibility reporting change. Methods: An interrupted time-series analysis was conducted. Among 1,491 patients who had positive urine cultures with susceptibilities and received at least 1 antibiotic with a listed UTI indication during their inpatient stay at UNCMC, we measured the weekly prevalence (%) of patients who received each antibiotic group: cephalexin, other oral β-lactams (amoxicillin-clavulanate, cefdinir, cefuroxime), fluoroquinolones (levofloxacin, ciprofloxacin), and ceftriaxone. The study comprised a preintervention period (September 2018–March 2019) and a postintervention period (September 2019–March 2020). The prevalence of each antibiotic or group was plotted over time, and segmented linear regression was used to estimate the impact of the intervention on each antibiotic groups’ time trend. Results: At study baseline in September 2018, the weekly prevalence of antibiotic use was 11% for cephalexin, 26% for other oral β-lactams, 51% for ceftriaxone, and 29% for fluoroquinolones. Fluoroquinolone use decreased steadily throughout the study period, by 11% during the 7-month preintervention period (95% CI, −17% to −5%) and by 8% (95% CI, −13% to −3%) after the intervention (P for trend deflection, .70). In contrast, during the preintervention period, trends were flat for cephalexin, ceftriaxone, and other oral β-lactams (all P for nonzero preintervention slope were >.40). During the postintervention period, use increased for ceftriaxone (6%; 95% CI, 3%–9%). Post-intervention use also increased for cephalexin (5%; 95% CI, −3% to 12%) and other oral β-lactams (4%; 95% CI, −8%, 15%), but these trends were imprecise and not statistically significant at α = .05. Fig. 1 displays trends and raw data for each antibiotic group. Conclusions: The urine culture susceptibility reporting change was associated with small increases in cephalexin and ceftriaxone use, coincident with continued decreasing use of fluoroquinolones, for hospitalized patients with positive urine cultures and a listed UTI indication. Low-resource EHR-based interventions may confer considerable benefit for antimicrobial stewardship efforts in this clinical setting, and larger real-world studies are needed to replicate and contextualize these findings.Funding: NoneDisclosures: None
Impact of exposure to potentially contaminated hospital beds on risk of hospital-onset C. difficile infection
Authors: Witt Lucy , Howard-Anderson Jessica , Overton Elizabeth , Jacob Jesse 
Published: May 2022

Background: Environmental contamination increases risk for Clostridioides difficile infection (CDI) given that spores can remain on a hospital bed, floor, sink, and light switch despite appropriate cleaning measures. Using real-time asset management software (AgileTrac, GE Healthcare) for beds we examined the risk of a patient developing hospital-onset CDI (HO-CDI) when staying in a hospital bed that had a previous occupant with CDI. Methods: We retrospectively identified all patients in tracked beds from April 2018 to August 2019 to identify hospital-onset CDI (HO-CDI), defined as a positive PCR test for C. difficile in a patient hospitalized for >3 days. A patient was defined as being exposed to a potentially “contaminated” bed if within the preceding 7 days from their HO-CDI diagnosis they resided in a hospital bed that, within the prior 90 days, had held an occupant with CDI (Fig. 1). We used multivariable logistic regression to evaluate the association between being exposed to a contaminated bed and HO-CDI. Model covariates were chosen a priori based on known risk factors for CDI. As a sensitivity analysis, we varied the length of time that a bed could stay contaminated from 90 to 60, 30, 14, and 7 days. Results: We analyzed 25,032 hospital encounters representing 18,860 unique patients; we identified 237 (0.9%) hospital encounters with HO-CDI (Table 1). The Elixhauser comorbidity score, being exposed to a contaminated bed, and receiving antibiotics or a proton pump inhibitor (PPI) during the hospital admission were all associated with HO-CDI in the univariable analysis (Table 2). In the adjusted multivariable model, being exposed to a contaminated bed remained a significant risk factor for HO-CDI (OR, 1.60; 95% CI, 1.22–2.08) even after controlling for known risk factors for CDI including age >65, elevated Elixhauser score, and recent antibiotic or PPI use (Table 2). In the sensitivity analysis in which we adjusted the time a bed was considered contaminated after CDI, being exposed to a contaminated bed remained a risk factor for HO-CDI, with a similar odds ratios as the original model (Table 2). Conclusions: Residing in a hospital bed that contained a previous occupant with CDI is a risk factor for developing HO-CDI. Hospital epidemiologists, infection control personnel, and environmental services staff should consider this association when developing CDI risk mitigation strategies.Funding: NoneDisclosures: None
Prescriptions patterns and appropriateness of usage of antibiotics in small and medium- sized hospitals in Korea
Authors: Kim Yong Chan , Park Ji Young , Kim Bongyoung , Kim Eu Suk , Ga Hyuk , Myung Rangmi , Park Se Yoon , Lee Myung Jin , Moon Song Mi , Park Sun Hee , Song Kyoung-Ho , Kim Hong Bin 
Published: May 2022

Background: Although small- and medium-sized hospitals comprise most healthcare providers in South Korea, data on antibiotic usage is limited in these facilities. We evaluated the pattern of antibiotic usage and its appropriateness in hospitals with <400 beds in South Korea. Methods: A multicenter retrospective study was conducted in 10 hospitals (6 long-term care hospitals, 3 acute-care hospitals, and 1 orthopedic hospital), with <400 beds in South Korea. We analyzed patterns of antibiotic prescription and their appropriateness in the participating hospitals. Data on the monthly antibiotic prescriptions and patient days for hospitalized patients were collected using electronic databases from each hospital. To avoid the effect of the COVID-19 pandemic, data were collected from January to December 2019. For the evaluation of the appropriateness of the prescription, 25 patients under antibiotic therapy were randomly selected at each hospital over 2 separate periods. Due to the heterogeneity of their characteristics, the orthopedics hospital was excluded from the analysis. The collected data were reviewed, and the appropriateness of antibiotic prescriptions was evaluated by 5 specialists in infectious diseases (adult and pediatric). Data from 2 hospitals were assigned to each specialist. The appropriateness of antibiotic prescriptions was evaluated from 3 aspects: route of administration, dose, and class. If the 3 aspects were ‘optimal,’ the prescription was considered ‘optimal.’ If only the route was ‘optimal,’ and the dose and/or class was ‘suboptimal,’ but not ‘inappropriate,’ it was considered ‘suboptimal.’ If even 1 aspect was ‘inappropriate,’ it was classified as ‘inappropriate.’ Results: The most commonly prescribed antibiotics in long-term care hospitals was fluoroquinolone, followed by β-lactam/β-lactamase inhibitor (antipseudomonal). In acute-care hospitals, these were third-generation cephalosporin, followed by first-generation cephalosporin and second-generation cephalosporin. The major antibiotics that were prescribed in the orthopedics hospital was first-generation cephalosporin. Only 2.3% of the antibiotics were administered inappropriately. In comparison, 15.3% of patients were prescribed an inappropriate dose. The proportion of inappropriate antibiotic prescriptions was 30.6% of the total antibiotic prescriptions. Conclusions: The antibiotic usage patterns vary between small- and medium-sized hospitals in South Korea. The proportion of inappropriate prescriptions exceeded 30% of the total antibiotic prescriptions.Funding: NoneDisclosures: None
Antibiotic use in end-of-life care patients: A nationwide Veterans’ Health Administration cohort study
Authors: Marra Alexandre , Clore Gosia , Balkenende Erin , Goedken Cassie , Livorsi Daniel , Goto Michihiko , Vaughan-Sarrazin  , Broderick Ann , Perencevich Eli 
Published: May 2022

Background: Antibiotic use during end-of-life (EOL) care is an increasingly important target for antimicrobial stewardship given the high prevalence of antibiotic use in this setting with limited evidence on safety and effectiveness to guide antibiotic decision making. We estimated antibiotic use during the last 6 months of life for patients under hospice or palliative care, and we identified potential targets (ie time points) during the EOL period when antimicrobial stewardship interventions could be targeted for maximal benefit. Methods: We conducted a retrospective cohort study of nationwide Veterans’ Affairs (VA) patients, 18 years and older who died between January 1, 2014, and December 31, 2019, and who had been hospitalized within 6 months prior to death. Data from the VA’s integrated electronic medical record (EMR) were collected including demographics, comorbid conditions, and duration of inpatient antibiotics administered, along with outpatient antibiotics dispensed. A propensity-score matched-cohort analysis was conducted to compare antibiotic use between patients placed into palliative care or hospice matched to patients not receiving palliative care or hospice care. Repeated measures ANOVA and repeated measures linear regression methods were used to analyze difference in difference (D-I-D) of days of therapy (DOT) between the 2 cohorts. Results: There were 251,822 patients in the cohort, including 23,746 in hospice care, 89,768 in palliative care, and 138,308 without palliative or hospice care. The median days from last discharge to death was 9 days. The most common comorbidities were chronic obstructive pulmonary diseases (50%), malignancy (46%), and diabetes mellitus (43%). Overall, 18,296 (77%) of 23,746 hospice patients, and 71,812 (80%) of 89,768 palliative care patients received at least 1 antibiotic, whereas 95,167 (69%) of 138,308 who were not placed in hospice or did not receive palliative care received antibiotics. In the primary matched cohort analysis that compared patients placed into hospice or palliative care to propensity-score matched controls, entry into palliative care was associated with a 11% absolute increase in antibiotic prescribing, and entry into hospice was associated with a 4% absolute increase during the 7–14 days after entry versus the 7–14 days before entry (Fig. 1). The stratified cohorts had very similar balanced covariates as the overall cohort. Conclusions: In our large cohort study, we observed that patients receiving EOL care had high levels of antibiotic exposure across VA population, particularly on entry to hospice or during admissions when they received palliative care consultation. Future studies are needed to identify the optimal EOL strategies for collaboration between antimicrobial stewardship and palliative care.Funding: NoneDisclosures: None