Risk factors for healthcare-associated candidemia in adults hospitalized with SARS-CoV-2 infection.

Analyzing data from a national deidentified electronic health record-based data set using a matched case-control study design, we found that antibiotic use and severity of illness were independent risk factors for healthcare-associated candidemia in adult patients hospitalized with SARS-CoV-2 infection. Interleukin-6 inhibitor and corticosteroid use were not independent risk factors.

Standardization of Emergency Department Clinical Note Templates: A Retrospective Analysis across an Integrated Health System.

BACKGROUND AND OBJECTIVE: Clinical documentation is essential for conveying medical decision-making, communication between providers and patients, and capturing quality, billing, and regulatory measures during emergency department (ED) visits. Growing evidence suggests the benefits of note template standardization; however, variations in documentation practices are common. The primary objective of this study is to measure the utilization and coding performance of a standardized ED note template implemented across a nine-hospital health system. METHODS: This was a retrospective study before and after the implementation of a standardized ED note template. A multi-disciplinary group consensus was built around standardized note elements, provider note workflows within the electronic health record (EHR), and how to incorporate newly required medical decision-making elements. The primary outcomes measured included the proportion of ED visits using standardized note templates, and the distribution of billing codes in the 6 months before and after implementation. RESULTS: In the preimplementation period, a total of six legacy ED note templates were being used across nine EDs, with the most used template accounting for approximately 36% of ED visits. Marked variations in documentation elements were noted across six legacy templates. After the implementation, 82% of ED visits system-wide used a single standardized note template. Following implementation, we observed a 1% increase in the proportion of ED visits coded as highest acuity and an unchanged proportion coded as second highest acuity. CONCLUSION: We observed a greater than twofold increase in the use of a standardized ED note template across a nine-hospital health system in anticipation of the new 2023 coding guidelines. The development and utilization of a standardized note template format relied heavily on multi-disciplinary stakeholder engagement to inform design that worked for varied documentation practices within the EHR. After the implementation of a standardized note template, we observed better-than-anticipated coding performance.

Structure and Funding of Clinical Informatics Fellowships: A National Survey of Program Directors.

BACKGROUND: In 2011, the American Board of Medical Specialties established clinical informatics (CI) as a subspecialty in medicine, jointly administered by the American Board of Pathology and the American Board of Preventive Medicine. Subsequently, many institutions created CI fellowship training programs to meet the growing need for informaticists. Although many programs share similar features, there is considerable variation in program funding and administrative structures. OBJECTIVES: The aim of our study was to characterize CI fellowship program features, including governance structures, funding sources, and expenses. METHODS: We created a cross-sectional online REDCap survey with 44 items requesting information on program administration, fellows, administrative support, funding sources, and expenses. We surveyed program directors of programs accredited by the Accreditation Council for Graduate Medical Education between 2014 and 2021. RESULTS: We invited 54 program directors, of which 41 (76%) completed the survey. The average administrative support received was $27,732/year. Most programs (85.4%) were accredited to have two or more fellows per year. Programs were administratively housed under six departments: Internal Medicine (17; 41.5%), Pediatrics (7; 17.1%), Pathology (6; 14.6%), Family Medicine (6; 14.6%), Emergency Medicine (4; 9.8%), and Anesthesiology (1; 2.4%). Funding sources for CI fellowship program directors included: hospital or health systems (28.3%), clinical departments (28.3%), graduate medical education office (13.2%), biomedical informatics department (9.4%), hospital information technology (9.4%), research and grants (7.5%), and other sources (3.8%) that included philanthropy and external entities. CONCLUSION: CI fellowships have been established in leading academic and community health care systems across the country. Due to their unique training requirements, these programs require significant resources for education, administration, and recruitment. There continues to be considerable heterogeneity in funding models between programs. Our survey findings reinforce the need for reformed federal funding models for informatics practice and training.

Twitter discussions on breastfeeding during the COVID-19 pandemic.

BACKGROUND: Breastfeeding is a critical health intervention in infants. Recent literature reported that the COVID-19 pandemic resulted in significant mental health issues in pregnant and breastfeeding women due to social isolation and lack of direct professional support. These maternal mental health issues affected infant nutrition and decreased breastfeeding rates during COVID-19. Twitter, a popular social media platform, can provide insight into public perceptions and sentiment about various health-related topics. With evidence of significant mental health issues among women during the COVID-19 pandemic, the perception of infant nutrition, specifically breastfeeding, remains unknown. METHODS: We aimed to understand public perceptions and sentiment regarding breastfeeding during the COVID-19 pandemic through Twitter analysis using natural language processing techniques. We collected and analyzed tweets related to breastfeeding and COVID-19 during the pandemic from January 2020 to May 2022. We used Python software (v3.9.0) for all data processing and analyses. We performed sentiment and emotion analysis of the tweets using natural language processing libraries and topic modeling using an unsupervised machine-learning algorithm. RESULTS: We analyzed 40,628 tweets related to breastfeeding and COVID-19 generated by 28,216 users. Emotion analysis revealed predominantly "Positive emotions" regarding breastfeeding, comprising 72% of tweets. The overall tweet sentiment was positive, with a mean weekly sentiment of 0.25 throughout, and was affected by external events. Topic modeling revealed six significant themes related to breastfeeding and COVID-19. Passive immunity through breastfeeding after maternal vaccination had the highest mean positive sentiment score of 0.32. CONCLUSIONS: Our study provides insight into public perceptions and sentiment regarding breastfeeding during the COVID-19 pandemic. Contrary to other topics we explored in the context of COVID (e.g., ivermectin, disinformation), we found that breastfeeding had an overall positive sentiment during the pandemic despite the documented rise in mental health challenges in pregnant and breastfeeding mothers. The wide range of topics on Twitter related to breastfeeding provides an opportunity for active engagement by the medical community and timely dissemination of advice, support, and guidance. Future studies should leverage social media analysis to gain real-time insight into public health topics of importance in child health and apply targeted interventions.

Assessing Racial and Ethnic Bias in Text Generation for Healthcare-Related Tasks by ChatGPT1.

Large Language Models (LLM) are AI tools that can respond human-like to voice or free-text commands without training on specific tasks. However, concerns have been raised about their potential racial bias in healthcare tasks. In this study, ChatGPT was used to generate healthcare-related text for patients with HIV, analyzing data from 100 deidentified electronic health record encounters. Each patient's data were fed four times with all information remaining the same except for race/ethnicity (African American, Asian, Hispanic White, Non-Hispanic White). The text output was analyzed for sentiment, subjectivity, reading ease, and most used words by race/ethnicity and insurance type. Results showed that instructions for African American, Asian, Hispanic White, and Non-Hispanic White patients had an average polarity of 0.14, 0.14, 0.15, and 0.14, respectively, with an average subjectivity of 0.46 for all races/ethnicities. The differences in polarity and subjectivity across races/ethnicities were not statistically significant. However, there was a statistically significant difference in word frequency across races/ethnicities and a statistically significant difference in subjectivity across insurance types with commercial insurance eliciting the most subjective responses and Medicare and other payer types the lowest. The study suggests that ChatGPT is relatively invariant to race/ethnicity and insurance type in terms of linguistic and readability measures. Further studies are needed to validate these results and assess their implications.

Is there an association between peri-diagnostic vaccination and clinical outcomes in COVID-19 patients?

Background: Peri-diagnostic vaccination contemporaneous with SARS-CoV-2 infection might boost antiviral immunity and improve patient outcomes. We investigated, among previously unvaccinated patients, whether vaccination (with the Pfizer, Moderna, or J&J vaccines) during the week before or after a positive COVID-19 test was associated with altered 30-day patient outcomes. Methods: Using a deidentified longitudinal EHR repository, we selected all previously unvaccinated adults who initially tested positive for SARS-CoV-2 between December 11, 2020 (the date of vaccine emergency use approval) and December 19, 2021. We assessed whether vaccination between days -7 and +7 of a positive test affected outcomes. The primary measure was progression to a more severe disease outcome within 30 days of diagnosis using the following hierarchy: hospitalization, intensive care, or death. Results: Among 60,031 hospitalized patients, 543 (0.91%) were initially vaccinated at the time of diagnosis and 59,488 (99.09%) remained unvaccinated during the period of interest. Among 316,337 nonhospitalized patients, 2,844 (0.90%) were initially vaccinated and 313,493 (99.1%) remained unvaccinated. In both analyses, individuals receiving vaccines were older, more often located in the northeast, more commonly insured by Medicare, and more burdened by comorbidities. Among previously unvaccinated patients, there was no association between receiving an initial vaccine dose between days -7 and +7 of diagnosis and progression to more severe disease within 30 days compared to patients who did not receive vaccines. Conclusions: Immunization during acute SARS-CoV-2 infection does not appear associated with clinical progression during the acute infectious period.

Risk Factors for SARS-CoV-2 Infection and Severe Outcomes Among People With Human Immunodeficiency Virus: Cohort Study.

Background: Studies on COVID-19 in people with HIV (PWH) have had limitations. Further investigations on risk factors and outcomes of SARS-CoV-2 infection among PWH are needed. Methods: This retrospective cohort study leveraged the national OPTUM COVID-19 data set to investigate factors associated with SARS-CoV-2 positivity among PWH and risk factors for severe outcomes, including hospitalization, intensive care unit stays, and death. A subset analysis was conducted to examine HIV-specific variables. Multiple variable logistic regression was used to adjust for covariates. Results: Of 43 173 PWH included in this study, 6472 had a positive SARS-CoV-2 result based on a polymerase chain reaction test or antigen test. For PWH with SARS-CoV-2 positivity, higher odds were found for those who were younger (18-49 years), Hispanic White, African American, from the US South, uninsured, and a noncurrent smoker and had a higher body mass index and higher Charlson Comorbidity Index. For PWH with severe outcomes, higher odds were identified for those who were SARS-CoV-2 positive, older, from the US South, receiving Medicaid/Medicare or uninsured, a current smoker, and underweight and had a higher Charlson Comorbidity Index. In a subset analysis including PWH with HIV care variables (n = 5098), those with unsuppressed HIV viral load, a low CD4 count, and no antiretroviral therapy had higher odds of severe outcomes. Conclusions: This large US study found significant ethnic, racial, and geographic differences in SARS-CoV-2 infection among PWH. Chronic comorbidities, older age, lower body mass index, and smoking were associated with severe outcomes among PWH during the COVID-19 pandemic. SARS-CoV-2 infection was associated with severe outcomes, but once we adjusted for HIV care variables, SARS-CoV-2 was no longer significant; however, low CD4 count, high viral load, and lack of antiretroviral therapy had higher odds of severe outcomes.

The lived experience of people with disabilities during the COVID-19 pandemic on Twitter: Content analysis.

Objective: People with disabilities (PWDs) are at greater risk of COVID-19 infection, complications, and death, and experience more difficulty accessing care. We analyzed Twitter tweets to identify important topics and investigate health policies' effects on PWDs. Methods: Twitter's application programming interface was used to access its public COVID-19 stream. English-language tweets from January 2020 to January 2022 containing a combination of keywords related to COVID-19, disability, discrimination, and inequity were collected and refined to exclude duplicates, replies, and retweets. The remaining tweets were analyzed for user demographics, content, and long-term availability. Results: The collection yielded 94,814 tweets from 43,296 accounts. During the observation period, 1068 (2.5%) accounts were suspended and 1088 (2.5%) accounts were deleted. Account suspension and deletion among verified users tweeting about COVID-19 and disability were 0.13% and 0.3%, respectively. Emotions were similar among active, suspended, and deleted users, with general negative and positive emotions most common followed by sadness, trust, anticipation, and anger. The overall average sentiment for the tweets was negative. Ten of the 12 topics identified (96.8%) related to pandemic effects on PWDs; "politics that rejects and leaves the disabled, elderly, and children behind" (48.3%) and "efforts to support PWDs in the COVID crisis" (31.8%) were most common. The sample of tweets by organizations (43.9%) was higher for this topic than for other COVID-19-related topics the authors have investigated. Conclusions: The primary discussion addressed how pandemic politics and policies disadvantage PWDs, older adults, and children, and secondarily expressed support for these populations. The increased level of Twitter use by organizations suggests a higher level of organization and advocacy within the disability community than in other groups. Twitter may facilitate recognition of increased harm to or discrimination against specific populations such as people living with disability during national health events.

Public perception of COVID-19 vaccines through analysis of Twitter content and users.

BACKGROUND: With the global continuation of the COVID-19 pandemic, the large-scale administration of a SARS-CoV-2 vaccine is crucial to achieve herd immunity and curtail further spread of the virus, but success is contingent on public understanding and vaccine uptake. We aim to understand public perception about vaccines for COVID-19 through the wide-scale, organic discussion on Twitter. METHODS: This cross-sectional observational study included Twitter posts matching the search criteria (('covid*' OR 'coronavirus') AND 'vaccine') posted during vaccine development from February 1st through December 11th, 2020. These COVID-19 vaccine related posts were analyzed with topic modeling, sentiment and emotion analysis, and demographic inference of users to provide insight into the evolution of public attitudes throughout the study period. FINDINGS: We evaluated 2,287,344 English tweets from 948,666 user accounts. Individuals represented 87.9 % (n = 834,224) of user accounts. Of individuals, men (n = 560,824) outnumbered women (n = 273,400) by 2:1 and 39.5 % (n = 329,776) of individuals were ≥40 years old. Daily mean sentiment fluctuated congruent with news events, but overall trended positively. Trust, anticipation, and fear were the three most predominant emotions; while fear was the most predominant emotion early in the study period, trust outpaced fear from April 2020 onward. Fear was more prevalent in tweets by individuals (26.3 % vs. organizations 19.4 %; p < 0.001), specifically among women (28.4 % vs. males 25.4 %; p < 0.001). Multiple topics had a monthly trend towards more positive sentiment. Tweets comparing COVID-19 to the influenza vaccine had strongly negative early sentiment but improved over time. INTERPRETATION: This study successfully explores sentiment, emotion, topics, and user demographics to elucidate important trends in public perception about COVID-19 vaccines. While public perception trended positively over the study period, some trends, especially within certain topic and demographic clusters, are concerning for COVID-19 vaccine hesitancy. These insights can provide targets for educational interventions and opportunity for continued real-time monitoring.

Analyzing an Emerging Pandemic on Twitter: Monkeypox.

Background: Social media platforms like Twitter provide important insights into the public's perceptions of global outbreaks like monkeypox. By analyzing tweets, we aimed to identify public knowledge and opinions on the monkeypox virus and related public health issues. Methods: We analyzed English-language tweets using the keyword "monkeypox" from 1 May to 23 July 2022. We reported gender, ethnicity, and race of Twitter users and analyzed tweets to identify predominant sentiment and emotions. We performed topic modeling and compared cohorts of users who self-identify as LGBTQ+ (an abreviation for lesbian, gay, bisexual, transgender, queer, and/or questioning) allies versus users who do not, and cohorts identified as "bots" versus humans. Results: A total of 48 330 tweets were written by LGBTQ+ self-identified advocates or allies. The mean sentiment score for all tweets was -0.413 on a -4 to +4 scale. Negative tweets comprised 39% of tweets. The most common emotions expressed were fear and sadness. Topic modeling identified unique topics among the 4 cohorts analyzed. Conclusions: The spread of mis- and disinformation about monkeypox was common in our tweet library. Various conspiracy theories about the origins of monkeypox, its relationship to global economic concerns, and homophobic and racial comments were common. Conversely, many other tweets helped to provide information about monkeypox vaccines, disease symptoms, and prevention methods. Discussion of rising monkeypox case numbers globally was also a large aspect of the conversation. Conclusions: We demonstrated that Twitter is an effective means of tracking sentiment about public healthcare issues. We gained insight into a subset of people, self-identified LGBTQ+ allies, who were more affected by monkeypox.

Incidence and Risk Factors for Severe Outcomes in Pediatric Patients With COVID-19.

OBJECTIVES: Throughout the pandemic, children with COVID-19 have experienced hospitalization, ICU admission, invasive respiratory support, and death. Using a multisite, national dataset, we investigate risk factors associated with these outcomes in children with COVID-19. METHODS: Our data source (Optum deidentified COVID-19 Electronic Health Record Dataset) included children aged 0 to 18 years testing positive for COVID-19 between January 1, 2020, and January 20, 2022. Using ordinal logistic regression, we identified factors associated with an ordinal outcome scale: nonhospitalization, hospitalization, or a severe composite outcome (ICU, intensive respiratory support, death). To contrast hospitalization for COVID-19 and incidental positivity on hospitalization, we secondarily identified patient factors associated with hospitalizations with a primary diagnosis of COVID-19. RESULTS: In 165 437 children with COVID-19, 3087 (1.8%) were hospitalized without complication, 2954 (1.8%) experienced ICU admission and/or intensive respiratory support, and 31 (0.02%) died. We grouped patients by age: 0 to 4 years old (35 088), and 5 to 11 years old (75 574), 12 to 18 years old (54 775). Factors positively associated with worse outcomes were preexisting comorbidities and residency in the Southern United States. In 0- to 4-year-old children, there was a nonlinear association between age and worse outcomes, with worse outcomes in 0- to 2-year-old children. In 5- to 18-year-old patients, vaccination was protective. Findings were similar in our secondary analysis of hospitalizations with a primary diagnosis of COVID-19, though region effects were no longer observed. CONCLUSIONS: Among children with COVID-19, preexisting comorbidities and residency in the Southern United States were positively associated with worse outcomes, whereas vaccination was negatively associated. Our study population was highly insured; future studies should evaluate underinsured populations to confirm generalizability.

Correction: The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.

[This corrects the article DOI: 10.2196/43623.].

Challenges in Forecasting Antimicrobial Resistance.

Antimicrobial resistance is a major threat to human health. Since the 2000s, computational tools for predicting infectious diseases have been greatly advanced; however, efforts to develop real-time forecasting models for antimicrobial-resistant organisms (AMROs) have been absent. In this perspective, we discuss the utility of AMRO forecasting at different scales, highlight the challenges in this field, and suggest future research priorities. We also discuss challenges in scientific understanding, access to high-quality data, model calibration, and implementation and evaluation of forecasting models. We further highlight the need to initiate research on AMRO forecasting using currently available data and resources to galvanize the research community and address initial practical questions.

The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.

BACKGROUND: Social connectedness decreases human mortality, improves cancer survival, cardiovascular health, and body mass, results in better-controlled glucose levels, and strengthens mental health. However, few public health studies have leveraged large social media data sets to classify user network structure and geographic reach rather than the sole use of social media platforms. OBJECTIVE: The objective of this study was to determine the association between population-level digital social connectedness and reach and depression in the population across geographies of the United States. METHODS: Our study used an ecological assessment of aggregated, cross-sectional population measures of social connectedness, and self-reported depression across all counties in the United States. This study included all 3142 counties in the contiguous United States. We used measures obtained between 2018 and 2020 for adult residents in the study area. The study's main exposure of interest is the Social Connectedness Index (SCI), a pair-wise composite index describing the "strength of connectedness between 2 geographic areas as represented by Facebook friendship ties." This measure describes the density and geographical reach of average county residents' social network using Facebook friendships and can differentiate between local and long-distance Facebook connections. The study's outcome of interest is self-reported depressive disorder as published by the Centers for Disease Control and Prevention. RESULTS: On average, 21% (21/100) of all adult residents in the United States reported a depressive disorder. Depression frequency was the lowest for counties in the Northeast (18.6%) and was highest for southern counties (22.4%). Social networks in northeastern counties involved moderately local connections (SCI 5-10 the 20th percentile for n=70, 36% of counties), whereas social networks in Midwest, southern, and western counties contained mostly local connections (SCI 1-2 the 20th percentile for n=598, 56.7%, n=401, 28.2%, and n=159, 38.4%, respectively). As the quantity and distance that social connections span (ie, SCI) increased, the prevalence of depressive disorders decreased by 0.3% (SE 0.1%) per rank. CONCLUSIONS: Social connectedness and depression showed, after adjusting for confounding factors such as income, education, cohabitation, natural resources, employment categories, accessibility, and urbanicity, that a greater social connectedness score is associated with a decreased prevalence of depression.

Reaching Populations at Risk for HIV Through Targeted Facebook Advertisements: Cost-Consequence Analysis.

BACKGROUND: An undiagnosed HIV infection remains a public health challenge. In the digital era, social media and digital health communication have been widely used to accelerate research, improve consumer health, and facilitate public health interventions including HIV prevention. OBJECTIVE: We aimed to evaluate and compare the projected cost and efficacy of different simulated Facebook (FB) advertisement (ad) approaches targeting at-risk populations for HIV based on new HIV diagnosis rates by age group and geographic region in the United States. METHODS: We used the FB ad platform to simulate (without actually launching) an automatically placed video ad for a 10-day duration targeting at-risk populations for HIV. We compared the estimated total ad audience, daily reach, daily clicks, and cost. We tested ads for the age group of 13 to 24 years (in which undiagnosed HIV is most prevalent), other age groups, US geographic regions and states, and different campaign budgets. We then estimated the ad cost per new HIV diagnosis based on HIV positivity rates and the average health care industry conversion rate. RESULTS: On April 20, 2021, the potential reach of targeted ads to at-risk populations for HIV in the United States was approximately 16 million for all age groups and 3.3 million for age group 13 to 24 years, with the highest potential reach in California, Texas, Florida, and New York. When using different FB ad budgets, the daily reach and daily clicks per US dollar followed a cumulative distribution curve of an exponential function. Using multiple US $10 ten-day ads, the cost per every new HIV diagnosis ranged from US $13.09 to US $37.82, with an average cost of US $19.45. In contrast, a 1-time national ad had a cost of US $72.76 to US $452.25 per new HIV diagnosis (mean US $166.79). The estimated cost per new HIV diagnosis ranged from US $13.96 to US $55.10 for all age groups (highest potential reach and lowest cost in the age groups 20-29 and 30-39 years) and from US $12.55 to US $24.67 for all US regions (with the highest potential reach of 6.2 million and the lowest cost per new HIV diagnosis at US $12.55 in the US South). CONCLUSIONS: Targeted personalized FB ads are a potential means to encourage at-risk populations for HIV to be tested, especially those aged 20 to 39 years in the US South, where the disease burden and potential reach on FB are high and the ad cost per new HIV diagnosis is low. Considering the cost efficiency of ads, the combined cost of multiple low-cost ads may be more economical than a single high-cost ad, suggesting that local FB ads could be more cost-effective than a single large-budget national FB ad.

Identifying the Optimal Look-back Period for Prior Antimicrobial Resistance Clinical Decision Support.

BACKGROUND: Lack of consensus on the appropriate look-back period for multi-drug resistance (MDR) complicates antimicrobial clinical decision support. We compared the predictive performance of different MDR look-back periods for five common MDR mechanisms (MRSA, VRE, ESBL, AmpC, CRE). METHODS: We mapped microbiological cultures to MDR mechanisms and labeled them at different look-back periods. We compared predictive performance for each look-back period-MDR combination using precision, recall, F1 scores, and odds ratios. RESULTS: Longer look-back periods resulted in lower odds ratios, lower precisions, higher recalls, and lower delta changes in precision and recall compared to shorter periods. We observed higher precision with more information available to clinicians. CONCLUSION: A previously positive MDR culture may have significant enough precision depending on the mechanism of resistance and varying information available. One year is a clinically relevant and statistically sound look-back period for empiric antimicrobial decision-making at varying points of care for the studied population.

Use of virtual care by infectious disease specialists in Canada: A national survey.

Objective: The aim of this study was to characterize the type and extent of virtual care use among infectious disease specialists in Canada, with a focus on the clinical factors that influence the decision to provide virtual versus in-person care. Methods: Infectious disease physicians practicing in Canada were invited to complete a survey regarding their experiences with virtual care. The survey included 14 vignettes depicting new outpatient and post-hospital-discharge referrals. Participants were asked to select which (if any) virtual care modalities they would feel comfortable using and to specify a reason if they did not feel comfortable providing care virtually. Machine learning and natural language processing techniques were used to identify themes. Results: In total, 57 infectious disease physicians completed the survey. Respondents reported devoting 36.5% (SD, 18.4%) of their infectious disease practice to outpatient care, with 44.2% (SD, 23.2%) of it being delivered virtually. Respondents were more comfortable providing virtual care to post-hospital-discharge referrals who had been seen by an infectious disease physician compared to new outpatient referrals. When respondents were not comfortable with using any virtual care modality, the following common themes emerged: the need for physical examination, the importance of establishing a therapeutic relationship, the need for additional in-person tests or diagnostics, and patient counselling. Conclusion: This study provides a glimpse into the current state of virtual care use in Canada and some of the major themes that affect decision making for virtual versus in-person care.

Clinically undetected polyclonal heteroresistance among Pseudomonas aeruginosa isolated from cystic fibrosis respiratory specimens.

BACKGROUND: Pseudomonas aeruginosa infection is the leading cause of death among patients with cystic fibrosis (CF) and a common cause of difficult-to-treat hospital-acquired infections. P. aeruginosa uses several mechanisms to resist different antibiotic classes and an individual CF patient can harbour multiple resistance phenotypes. OBJECTIVES: To determine the rates and distribution of polyclonal heteroresistance (PHR) in P. aeruginosa by random, prospective evaluation of respiratory cultures from CF patients at a large referral centre over a 1 year period. METHODS: We obtained 28 unique sputum samples from 19 CF patients and took multiple isolates from each, even when morphologically similar, yielding 280 unique isolates. We performed antimicrobial susceptibility testing (AST) on all isolates and calculated PHR on the basis of variability in AST in a given sample. We then performed whole-genome sequencing on 134 isolates and used a machine-learning association model to interrogate phenotypic PHR from genomic data. RESULTS: PHR was identified in most sampled patients (n = 15/19; 79%). Importantly, resistant phenotypes were not detected by routine AST in 26% of patients (n = 5/19). The machine-learning model, using the extended sampling, identified at least one genetic variant associated with phenotypic resistance in 94.3% of isolates (n = 1392/1476). CONCLUSION: PHR is common among P. aeruginosa in the CF lung. While traditional microbiological methods often fail to detect resistant subpopulations, extended sampling of isolates and conventional AST identified PHR in most patients. A machine-learning tool successfully identified at least one resistance variant in almost all resistant isolates by leveraging this extended sampling and conventional AST.

The Texas Health Resources Clinical Scholars Program: Learning healthcare system workforce development through embedded translational research.

Introduction: Texas Health Resources (THR), a large, nonprofit health care system based in the Dallas-Fort Worth area, has collaborated with the University of Texas Southwestern Medical Center (UTSW) to develop and operate a unique, integrated approach for Learning Health System (LHS) workforce development. This training model centers on academic health system faculty members conducting later-stage translational research within a partnering regional care delivery organization. Methods: The THR Clinical Scholars Program engages early career UTSW faculty members to conduct studies that are likely to have an impact on care delivery at the health system level. Interested candidates submit formal applications to the program. A joint committee comprised of senior research faculty from UTSW and THR clinical leadership reviews proposals with a focus on the shared LHS needs of both institutions-developing high quality research output that can be applied to enhance care delivery. A key prioritization criterion for funding is the degree to which the research addresses a question relevant to THR as a high-volume network with multiple channels for consumers to access care. The program emphasis is on supporting embedded research initiatives using health system data to generate knowledge that will improve the quality and efficiency of care for the patient populations served by the participant organizations. Results: We discuss specific strategic and tactical components of the THR Clinical Scholars Program including an overview of the academic affiliation agreement between the collaborating organizations, criteria for successful program applications, data sharing, and funding. We also share project summaries from selected clinical scholars as examples of the LHS research done in the program to date. Conclusion: This experience report provides an implementation framework for other academic health systems interested in adopting similar LHS workforce training models with community partners.