Implementation of contact precautions for multidrug-resistant organisms in the post-COVID-19 pandemic era: An updated national Emerging Infections Network (EIN) survey.

OBJECTIVE: To understand how healthcare facilities employ contact precautions for patients with multidrug-resistant organisms (MDROs) in the post-coronavirus disease 2019 (COVID-19) era and explore changes since 2014. DESIGN: Cross-sectional survey. PARTICIPANTS: Emerging Infections Network (EIN) physicians involved in infection prevention or hospital epidemiology. METHODS: In September 2022, we sent via email an 8-question survey on contact precautions and adjunctive measures to reduce MDRO transmission in inpatient facilities. We also asked about changes since the COVID-19 pandemic. We used descriptive statistics to summarize data and compared results to a similar survey administered in 2014. RESULTS: Of 708 EIN members, 283 (40%) responded to the survey and 201 reported working in infection prevention. A majority of facilities (66% and 69%) routinely use contact precautions for methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) respectively, compared to 93% and 92% in 2014. Nearly all (>90%) use contact precautions for Candida auris, carbapenem-resistant Enterobacterales (CRE), and carbapenem-resistant Acinetobacter baumannii. More variability was reported for carbapenem-resistant Pseudomonas aeruginosa and extended-spectrum ß-lactamase-producing gram-negative organisms. Compared to 2014, fewer hospitals perform active surveillance for MRSA and VRE. Overall, 90% of facilities used chlorhexidine gluconate bathing in all or select inpatients, and 53% used ultraviolet light or hydrogen peroxide vapor disinfection at discharge. Many respondents (44%) reported changes to contact precautions since COVID-19 that remain in place. CONCLUSIONS: Heterogeneity exists in the use of transmission-based precautions and adjunctive infection prevention measures aimed at reducing MDRO transmission. This variation reflects a need for updated and specific guidance, as well as further research on the use of contact precautions in healthcare facilities.

Strategies for developing a successful career in academic medicine.

Academic medicine provides physicians an opportunity for long-term career satisfaction and fulfillment. However, despite the potential for great reward, academic careers can be challenging. To better define approaches to successfully navigate academic medicine, the Southern Society for Clinical Investigation sponsored a workshop titled 'Successful Careers in Academic Medicine' during the 2023 Southern Regional Meeting held in New Orleans; the critical elements of which are highlighted in the following summary. Participants discussed the benefits of an academic career, summarized strategies for negotiating a job, listed critical tools for career development, and discussed key concepts about planning and navigating the academic medicine promotion process. The information provides a roadmap for physicians to develop successful careers in academic medicine.

The impact of COVID-19 on multidrug-resistant organisms causing healthcare-associated infections: a narrative review.

Coronavirus disease 2019 (COVID-19) changed healthcare across the world. With this change came an increase in healthcare-associated infections (HAIs) and a concerning concurrent proliferation of MDR organisms (MDROs). In this narrative review, we describe the impact of COVID-19 on HAIs and MDROs, describe potential causes of these changes, and discuss future directions to combat the observed rise in rates of HAIs and MDRO infections.

A Final Frontier in Environment-Genome Interactions? Integrated, Multi-Omic Approaches to Predictions of Non-Communicable Disease Risk.

Epidemiological and associative research from humans and animals identifies correlations between the environment and health impacts. The environment-health inter-relationship is effected through an individual's underlying genetic variation and mediated by mechanisms that include the changes to gene regulation that are associated with the diversity of phenotypes we exhibit. However, the causal relationships have yet to be established, in part because the associations are reduced to individual interactions and the combinatorial effects are rarely studied. This problem is exacerbated by the fact that our genomes are highly dynamic; they integrate information across multiple levels (from linear sequence, to structural organisation, to temporal variation) each of which is open to and responds to environmental influence. To unravel the complexities of the genomic basis of human disease, and in particular non-communicable diseases that are also influenced by the environment (e.g., obesity, type II diabetes, cancer, multiple sclerosis, some neurodegenerative diseases, inflammatory bowel disease, rheumatoid arthritis) it is imperative that we fully integrate multiple layers of genomic data. Here we review current progress in integrated genomic data analysis, and discuss cases where data integration would lead to significant advances in our ability to predict how the environment may impact on our health. We also outline limitations which should form the basis of future research questions. In so doing, this review will lay the foundations for future research into the impact of the environment on our health.

Occupational risk factors for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among healthcare personnel: A 6-month prospective analysis of the COVID-19 Prevention in Emory Healthcare Personnel (COPE) Study.

OBJECTIVES: To determine the incidence of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among healthcare personnel (HCP) and to assess occupational risks for SARS-CoV-2 infection. DESIGN: Prospective cohort of healthcare personnel (HCP) followed for 6 months from May through December 2020. SETTING: Large academic healthcare system including 4 hospitals and affiliated clinics in Atlanta, Georgia. PARTICIPANTS: HCP, including those with and without direct patient-care activities, working during the coronavirus disease 2019 (COVID-19) pandemic. METHODS: Incident SARS-CoV-2 infections were determined through serologic testing for SARS-CoV-2 IgG at enrollment, at 3 months, and at 6 months. HCP completed monthly surveys regarding occupational activities. Multivariable logistic regression was used to identify occupational factors that increased the risk of SARS-CoV-2 infection. RESULTS: Of the 304 evaluable HCP that were seronegative at enrollment, 26 (9%) seroconverted for SARS-CoV-2 IgG by 6 months. Overall, 219 participants (73%) self-identified as White race, 119 (40%) were nurses, and 121 (40%) worked on inpatient medical-surgical floors. In a multivariable analysis, HCP who identified as Black race were more likely to seroconvert than HCP who identified as White (odds ratio, 4.5; 95% confidence interval, 1.3-14.2). Increased risk for SARS-CoV-2 infection was not identified for any occupational activity, including spending >50% of a typical shift at a patient's bedside, working in a COVID-19 unit, or performing or being present for aerosol-generating procedures (AGPs). CONCLUSIONS: In our study cohort of HCP working in an academic healthcare system, <10% had evidence of SARS-CoV-2 infection over 6 months. No specific occupational activities were identified as increasing risk for SARS-CoV-2 infection.

Poor outcomes in both infection and colonization with carbapenem-resistant Enterobacterales.

OBJECTIVES: To describe the epidemiology of patients with nonintestinal carbapenem-resistant Enterobacterales (CRE) colonization and to compare clinical outcomes of these patients to those with CRE infection. DESIGN: A secondary analysis of Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacteriaceae 2 (CRACKLE-2), a prospective observational cohort. SETTING: A total of 49 US short-term acute-care hospitals. PATIENTS: Patients hospitalized with CRE isolated from clinical cultures, April, 30, 2016, through August 31, 2017. METHODS: We described characteristics of patients in CRACKLE-2 with nonintestinal CRE colonization and assessed the impact of site of colonization on clinical outcomes. We then compared outcomes of patients defined as having nonintestinal CRE colonization to all those defined as having infection. The primary outcome was a desirability of outcome ranking (DOOR) at 30 days. Secondary outcomes were 30-day mortality and 90-day readmission. RESULTS: Of 547 patients with nonintestinal CRE colonization, 275 (50%) were from the urinary tract, 201 (37%) were from the respiratory tract, and 71 (13%) were from a wound. Patients with urinary tract colonization were more likely to have a more desirable clinical outcome at 30 days than those with respiratory tract colonization, with a DOOR probability of better outcome of 61% (95% confidence interval [CI], 53%-71%). When compared to 255 patients with CRE infection, patients with CRE colonization had a similar overall clinical outcome, as well as 30-day mortality and 90-day readmission rates when analyzed in aggregate or by culture site. Sensitivity analyses demonstrated similar results using different definitions of infection. CONCLUSIONS: Patients with nonintestinal CRE colonization had outcomes similar to those with CRE infection. Clinical outcomes may be influenced more by culture site than classification as "colonized" or "infected."

Occupational risk factors for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among healthcare personnel: A cross-sectional analysis of subjects enrolled in the COVID-19 Prevention in Emory Healthcare Personnel (COPE) study.

Among 353 healthcare personnel in a longitudinal cohort in 4 hospitals in Atlanta, Georgia (May-June 2020), 23 (6.5%) had severe acute respiratory coronavirus virus 2 (SARS-CoV-2) antibodies. Spending >50% of a typical shift at the bedside (OR, 3.4; 95% CI, 1.2-10.5) and black race (OR, 8.4; 95% CI, 2.7-27.4) were associated with SARS-CoV-2 seropositivity.

Healthcare worker mental models of patient care tasks in the context of infection prevention and control.

OBJECTIVE: Understanding the cognitive determinants of healthcare worker (HCW) behavior is important for improving the use of infection prevention and control (IPC) practices. Given a patient requiring only standard precautions, we examined the dimensions along which different populations of HCWs cognitively organize patient care tasks (ie, their mental models). DESIGN: HCWs read a description of a patient and then rated the similarities of 25 patient care tasks from an infection prevention perspective. Using multidimensional scaling, we identified the dimensions (ie, characteristics of tasks) underlying these ratings and the salience of each dimension to HCWs. SETTING: Adult inpatient hospitals across an academic hospital network. PARTICIPANTS: In total, 40 HCWs, comprising infection preventionists and nurses from intensive care units, emergency departments, and medical-surgical floors rated the similarity of tasks. To identify the meaning of each dimension, another 6 nurses rated each task in terms of specific characteristics of tasks. RESULTS: Each HCW population perceived patient care tasks to vary along 3 common dimensions; most salient was the perceived magnitude of infection risk to the patient in a task, followed by the perceived dirtiness and risk of HCW exposure to body fluids, and lastly, the relative importance of a task for preventing versus controlling an infection in a patient. CONCLUSIONS: For a patient requiring only standard precautions, different populations of HCWs have similar mental models of how various patient care tasks relate to IPC. Techniques for eliciting mental models open new avenues for understanding and ultimately modifying the cognitive determinants of IPC behaviors.

An assessment of uranium in groundwater in the Grand Canyon region.

The Grand Canyon region in northern Arizona is a home or sacred place of origin for many Native Americans and is visited by over 6 million tourists each year. Most communities in the area depend upon groundwater for all water uses. Some of the highest-grade uranium ore in the United States also is found in the Grand Canyon region. A withdrawal of over 4000 km2 of Federal land in the Grand Canyon region from new uranium mining activities for 20 years was instituted in 2012, owing in part to a lack of scientific data on potential effects from uranium mining on water resources in the area. The U.S. Geological Survey has collected groundwater chemistry samples since 1981 in the Grand Canyon region to better understand the current state of groundwater quality, to monitor for changes in groundwater quality that may be the result of mining activities, and to identify "hot spots" with elevated metal concentrations and investigate the causes. This manuscript presents results for the assessment of uranium in groundwater in the Grand Canyon region. Analytical results for uranium in groundwater in the Grand Canyon region were available for 573 samples collected from 180 spring sites and 26 wells from September 1, 1981 to October 7, 2020. Samples were collected from springs issuing from stratigraphic units above, within, and below the Permian strata that host uranium ore in breccia pipes in the area. Maximum uranium concentrations at groundwater sites in the region ranged from less than 1 µg/L at 23 sites (11%) to 100 µg/L or more at 4 sites (2%). Of the 206 groundwater sites sampled, 195 sites (95%) had maximum observed uranium concentrations less than the U.S. Environmental Protection Agency's Maximum Contaminant Level of 30 µg/L for drinking water and 177 sites (86%) had uranium concentrations less than the 15 µg/L Canadian benchmark for protection of aquatic life in freshwater. The establishment of baseline groundwater quality is an important first step in monitoring for change in water chemistry throughout mining lifecycles and beyond to ensure the health of these critical groundwater resources.

Carbapenem-resistant Enterobacterales bacteriuria and subsequent bacteremia: A population-based study.

OBJECTIVE: To describe the epidemiology of carbapenem-resistant Enterobacterales (CRE) bacteriuria and to determine whether urinary catheters increase the risk of subsequent CRE bacteremia. DESIGN: Using active population- and laboratory-based surveillance we described a cohort of patients with incident CRE bacteriuria and identified risk factors for developing CRE bacteremia within 1 year. SETTING: The study was conducted among the 8 counties of Georgia Health District 3 (HD3) in Atlanta, Georgia. PATIENTS: Residents of HD3 with CRE first identified in urine between 2012 and 2017. RESULTS: We identified 464 patients with CRE bacteriuria (mean yearly incidence, 1.96 cases per 100,000 population). Of 425 with chart review, most had a urinary catheter (56%), and many resided in long-term care facilities (48%), had a Charlson comorbidity index >3 (38%) or a decubitus ulcer (37%). 21 patients (5%) developed CRE bacteremia with the same organism within 1 year. Risk factors for subsequent bacteremia included presence of a urinary catheter (odds ratio [OR], 8.0; 95% confidence interval [CI], 1.8-34.9), central venous catheter (OR, 4.3; 95% CI, 1.7-10.6) or another indwelling device (OR, 4.3; 95% CI, 1.6-11.4), urine culture obtained as an inpatient (OR, 5.7; 95% CI, 1.3-25.9), and being in the ICU in the week prior to urine culture (OR, 2.9; 95% CI, 1.1-7.8). In a multivariable analysis, urinary catheter increased the risk of CRE bacteremia (OR, 5.3; 95% CI, 1.2-23.6). CONCLUSIONS: In patients with CRE bacteriuria, urinary catheters increase the risk of CRE bacteremia. Future interventions should aim to reduce inappropriate insertion and early removal of urinary catheters.

Assessing uranium and select trace elements associated with breccia pipe uranium deposits in the Colorado River and main tributaries in Grand Canyon, USA.

Assessing chemical loading from streams in remote, difficult-to-access watersheds is challenging. The Grand Canyon area in northern Arizona, an international tourist destination and sacred place for many Native Americans, is characterized by broad plateaus divided by canyons as much as two-thousand meters deep and hosts some of the highest-grade uranium deposits in the U.S. From 2015-2018 major surface waters in Grand Canyon were monitored for select elements associated with breccia-pipe uranium deposits in the area, including uranium, arsenic, cadmium, and lead. Dissolved constituents in the Colorado River were monitored upstream (Lees Ferry), in the middle (Phantom Ranch), and downstream (Diamond Creek) of uranium mining areas. Concentrations of uranium, arsenic, cadmium, and lead at these main-stem sites varied little during the study period and were all well below human health and aquatic life benchmark criteria (30, 10, 5, and 15 µg/L maximum contaminant levels and 15, 150, 0.8, and 3.1 µg/L aquatic life criteria, respectively). Additionally, dissolved and sediment-bound constituents were monitored during a wide range of streamflow conditions at Little Colorado River, Kanab Creek, and Havasu Creek tributaries, whose watersheds have experienced different levels of uranium mining activities over time. Samples from the tributary sites contained ≤3.8 µg/L of dissolved cadmium and lead, and ≤17 µg/L of dissolved uranium. Dissolved arsenic also was mostly below human and aquatic life criteria at Little Colorado River and Kanab Creek; however, 63% of water samples from Havasu Creek were above the maximum contaminant level for arsenic. Arsenic in suspended sediment was greater than sediment quality guidelines in 9%, 35%, and 35% of samples from Little Colorado River, Kanab Creek, and Havasu Creek, respectively. At the concentrations observed during this study, tributaries contributed on average only about 0.12 µg/L of arsenic and 0.03 µg/L of uranium to the main-stem river. This study demonstrates how chemical loading from mined watersheds may be reliably assessed across a wide range of flow conditions in challenging locations.

The impact of an electronic medical record nudge on reducing testing for hospital-onset Clostridioides difficile infection.

OBJECTIVE: To determine the effect of an electronic medical record (EMR) nudge at reducing total and inappropriate orders testing for hospital-onset Clostridioides difficile infection (HO-CDI). DESIGN: An interrupted time series analysis of HO-CDI orders 2 years before and 2 years after the implementation of an EMR intervention designed to reduce inappropriate HO-CDI testing. Orders for C. difficile testing were considered inappropriate if the patient had received a laxative or stool softener in the previous 24 hours. SETTING: Four hospitals in an academic healthcare network. PATIENTS: All patients with a C. difficile order after hospital day 3. INTERVENTION: Orders for C. difficile testing in patients administered a laxative or stool softener in <24 hours triggered an EMR alert defaulting to cancellation of the order ("nudge"). RESULTS: Of the 17,694 HO-CDI orders, 7% were inappropriate (8% prentervention vs 6% postintervention; P < .001). Monthly HO-CDI orders decreased by 21% postintervention (level-change rate ratio [RR], 0.79; 95% confidence interval [CI], 0.73-0.86), and the rate continued to decrease (postintervention trend change RR, 0.99; 95% CI, 0.98-1.00). The intervention was not associated with a level change in inappropriate HO-CDI orders (RR, 0.80; 95% CI, 0.61-1.05), but the postintervention inappropriate order rate decreased over time (RR, 0.95; 95% CI, 0.93-0.97). CONCLUSION: An EMR nudge to minimize inappropriate ordering for C. difficile was effective at reducing HO-CDI orders, and likely contributed to decreasing the inappropriate HO-CDI order rate after the intervention.

Sustained decrease in urine culture utilization after implementing a reflex urine culture intervention: A multicenter quasi-experimental study.

Accurately diagnosing urinary tract infections (UTIs) in hospitalized patients remains challenging, requiring correlation of frequently nonspecific symptoms and laboratory findings. Urine cultures (UCs) are often ordered indiscriminately, especially in patients with urinary catheters, despite the Infectious Diseases Society of America guidelines recommending against routine screening for asymptomatic bacteriuria (ASB).1,2 Positive UCs can be difficult for providers to ignore, leading to unnecessary antibiotic treatment of ASB.2,3 Using diagnostic stewardship to limit UCs to situations with a positive urinalysis (UA) can reduce inappropriate UCs since the absence of pyuria suggests the absence of infection.4-6 We assessed the impact of the implementation of a UA with reflex to UC algorithm ("reflex intervention") on UC ordering practices, diagnostic efficiency, and UTIs using a quasi-experimental design.

Analytical performance of Envisia: a genomic classifier for usual interstitial pneumonia.

BACKGROUND: Clinical guidelines specify that diagnosis of interstitial pulmonary fibrosis (IPF) requires identification of usual interstitial pneumonia (UIP) pattern. While UIP can be identified by high resolution CT of the chest, the results are often inconclusive, making surgical lung biopsy necessary to reach a definitive diagnosis (Raghu et al., Am J Respir Crit Care Med 183(6):788-824, 2011). The Envisia genomic classifier differentiates UIP from non-UIP pathology in transbronchial biopsies (TBB), potentially allowing patients to avoid an invasive procedure (Brown et al., Am J Respir Crit Care Med 195:A6792, 2017). To ensure patient safety and efficacy, a laboratory developed test (LDT) must meet strict regulatory requirements for accuracy, reproducibility and robustness. The analytical characteristics of the Envisia test are assessed and reported here. METHODS: The Envisia test utilizes total RNA extracted from TBB samples to perform Next Generation RNA Sequencing. The gene count data from 190 genes are then input to the Envisia genomic classifier, a machine learning algorithm, to output either a UIP or non-UIP classification result. We characterized the stability of RNA in TBBs during collection and shipment, and evaluated input RNA mass and proportions on the limit of detection of UIP. We evaluated potentially interfering substances such as blood and genomic DNA. Intra-run, inter-run, and inter-laboratory reproducibility of test results were also characterized. RESULTS: RNA content within TBBs preserved in RNAprotect is stable for up to 14 days with no detectable change in RNA quality. The Envisia test is tolerant to variation in RNA input (5 to 30 ng), with no impact on classifier results. The Envisia test can tolerate dilution of non-UIP and UIP classification signals at the RNA level by up to 60% and 20%, respectively. Analytical specificity studies utilizing UIP and non-UIP samples mixed with genomic DNA (up to 30% relative input) demonstrated no impact to classifier results. The Envisia test tolerates up to 22% of blood contamination, well beyond the level observed in TBBs. The test is reproducible from RNA extraction through to Envisia test result (standard deviation of 0.20 for Envisia classification scores on > 7-unit scale). CONCLUSIONS: The Envisia test demonstrates the robust analytical performance required of an LDT. Envisia can be used to inform the diagnoses of patients with suspected IPF.

Analytical performance of a bronchial genomic classifier.

BACKGROUND: The current standard practice of lung lesion diagnosis often leads to inconclusive results, requiring additional diagnostic follow up procedures that are invasive and often unnecessary due to the high benign rate in such lesions (Chest 143:e78S-e92, 2013). The Percepta bronchial genomic classifier was developed and clinically validated to provide more accurate classification of lung nodules and lesions that are inconclusive by bronchoscopy, using bronchial brushing specimens (N Engl J Med 373:243-51, 2015, BMC Med Genomics 8:18, 2015). The analytical performance of the Percepta test is reported here. METHODS: Analytical performance studies were designed to characterize the stability of RNA in bronchial brushing specimens during collection and shipment; analytical sensitivity defined as input RNA mass; analytical specificity (i.e. potentially interfering substances) as tested on blood and genomic DNA; and assay performance studies including intra-run, inter-run, and inter-laboratory reproducibility. RESULTS: RNA content within bronchial brushing specimens preserved in RNAprotect is stable for up to 20 days at 4 °C with no changes in RNA yield or integrity. Analytical sensitivity studies demonstrated tolerance to variation in RNA input (157 ng to 243 ng). Analytical specificity studies utilizing cancer positive and cancer negative samples mixed with either blood (up to 10 % input mass) or genomic DNA (up to 10 % input mass) demonstrated no assay interference. The test is reproducible from RNA extraction through to Percepta test result, including variation across operators, runs, reagent lots, and laboratories (standard deviation of 0.26 for scores on > 6 unit scale). CONCLUSIONS: Analytical sensitivity, analytical specificity and robustness of the Percepta test were successfully verified, supporting its suitability for clinical use.