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Long-acting injectable (LAI) antiretroviral therapy (ART) is available to people with HIV (PWH), but it is unknown which PWH prefer this option. Using the Andersen Behavioral Model this study identifies characteristics of PWH with greater preference for LAI ART. Cross-sectional data from the Florida Cohort, which enrolled adult PWH from community-based clinics included information on predisposing (demographics), enabling (transportation, income), and need (ART adherence <90%) factors. ART preference was assessed via a single question (prefer pills, quarterly LAI, or no preference). Confounder-adjusted multinomial logistic regressions compared those who preferred pills to the other preference options, with covariates identified using directed acyclic graphs. Overall, 314 participants responded (40% non-Hispanic Black, 62% assigned male, 63% aged 50+). Most (63%) preferred the hypothetical LAI, 23% preferred pills, and 14% had no preference. PWH with access to a car (aRRR 1.97 95%CI 1.05-3.71), higher income (aRRR 2.55 95%CI 1.04-6.25), and suboptimal ART adherence (aRRR 7.41 95% CI 1.52-36.23) were more likely to prefer the LAI, while those who reported having no social network were less likely to prefer the LAI (aRRR 0.32 95% CI 0.11-0.88). Overall LAI interest was high, with greater preference associated with enabling and need factors.
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Respiratory tract infections are a serious threat to health, especially in the presence of antimicrobial resistance (AMR). Existing AMR detection methods are limited by slow turnaround times and low accuracy due to the presence of false positives and negatives. In this study, we simulate 1,116 clinical metagenomics samples on both Illumina and Nanopore sequencing from curated, real-world sequencing of A. baumannii respiratory infections and build AI models to predict resistance to amikacin. The best performance is achieved by XGBoost on Illumina sequencing (area under the ROC curve = 0.7993 on 5-fold cross-validation).
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Acinetobacter baumannii , Amicacina , Farmacorresistência Bacteriana , Metagenômica , Amicacina/farmacologia , Amicacina/uso terapêutico , Acinetobacter baumannii/efeitos dos fármacos , Acinetobacter baumannii/genética , Humanos , Farmacorresistência Bacteriana/genética , Infecções Respiratórias/tratamento farmacológico , Infecções Respiratórias/microbiologia , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Infecções por Acinetobacter/tratamento farmacológico , Infecções por Acinetobacter/microbiologiaRESUMO
Molecular data analysis is invaluable in understanding the overall behavior of a rapidly spreading virus population when epidemiological surveillance is problematic. It is also particularly beneficial in describing subgroups within the population, often identified as clades within a phylogenetic tree that represent individuals connected via direct transmission or transmission via differing risk factors in viral spread. However, transmission patterns or viral dynamics within these smaller groups should not be expected to exhibit homogeneous behavior over time. As such, standard phylogenetic approaches that identify clusters based on summary statistics would not be expected to capture dynamic clusters of transmission. We, therefore, sought to evaluate the performance of existing and adapted phylogeny-based cluster identification tools on simulated transmission clusters exhibiting dynamic transmission behavior over time. Despite the complementarity of the tools, we provide strong evidence that novel cluster identification methods are needed for reliable detection of epidemiologically linked individuals, particularly those exhibiting changing transmission dynamics during dynamic outbreak scenarios.
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MOTIVATION: World Health Organization estimates that there were over 10 million cases of tuberculosis (TB) worldwide in 2019, resulting in over 1.4 million deaths, with a worrisome increasing trend yearly. The disease is caused by Mycobacterium tuberculosis (MTB) through airborne transmission. Treatment of TB is estimated to be 85% successful, however, this drops to 57% if MTB exhibits multiple antimicrobial resistance (AMR), for which fewer treatment options are available. RESULTS: We develop a robust machine-learning classifier using both linear and nonlinear models (i.e. LASSO logistic regression (LR) and random forests (RF)) to predict the phenotypic resistance of Mycobacterium tuberculosis (MTB) for a broad range of antibiotic drugs. We use data from the CRyPTIC consortium to train our classifier, which consists of whole genome sequencing and antibiotic susceptibility testing (AST) phenotypic data for 13 different antibiotics. To train our model, we assemble the sequence data into genomic contigs, identify all unique 31-mers in the set of contigs, and build a feature matrix M, where M[i, j] is equal to the number of times the ith 31-mer occurs in the jth genome. Due to the size of this feature matrix (over 350 million unique 31-mers), we build and use a sparse matrix representation. Our method, which we refer to as MTB++, leverages compact data structures and iterative methods to allow for the screening of all the 31-mers in the development of both LASSO LR and RF. MTB++ is able to achieve high discrimination (F-1 >80%) for the first-line antibiotics. Moreover, MTB++ had the highest F-1 score in all but three classes and was the most comprehensive since it had an F-1 score >75% in all but four (rare) antibiotic drugs. We use our feature selection to contextualize the 31-mers that are used for the prediction of phenotypic resistance, leading to some insights about sequence similarity to genes in MEGARes. Lastly, we give an estimate of the amount of data that is needed in order to provide accurate predictions. AVAILABILITY: The models and source code are publicly available on Github at https://github.com/M-Serajian/MTB-Pipeline.
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Aprendizado de Máquina , Mycobacterium tuberculosis , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/efeitos dos fármacos , Farmacorresistência Bacteriana/genética , Testes de Sensibilidade Microbiana , Antibacterianos/farmacologia , Sequenciamento Completo do Genoma/métodos , Genoma Bacteriano , HumanosRESUMO
In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks and patterns of spread is critical to inform public health programs. Projections of transmission growth or decline among specific risk groups can aid in optimizing interventions, particularly when resources are limited. Phylogenetic trees have been widely used in the detection of transmission chains and high-risk populations. Moreover, tree topology and the incorporation of population parameters (phylodynamics) can be useful in reconstructing the evolutionary dynamics of an epidemic across space and time among individuals. We now demonstrate the utility of phylodynamic trees for transmission modeling and forecasting, developing a phylogeny-based deep learning system, referred to as DeepDynaForecast. Our approach leverages a primal-dual graph learning structure with shortcut multi-layer aggregation, which is suited for the early identification and prediction of transmission dynamics in emerging high-risk groups. We demonstrate the accuracy of DeepDynaForecast using simulated outbreak data and the utility of the learned model using empirical, large-scale data from the human immunodeficiency virus epidemic in Florida between 2012 and 2020. Our framework is available as open-source software (MIT license) at github.com/lab-smile/DeepDynaForcast.
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Biologia Computacional , Aprendizado Profundo , Epidemias , Filogenia , Humanos , Epidemias/estatística & dados numéricos , Biologia Computacional/métodos , Infecções por HIV/transmissão , Infecções por HIV/epidemiologia , Software , Florida/epidemiologia , Algoritmos , Simulação por Computador , Surtos de Doenças/estatística & dados numéricosRESUMO
Portable genomic sequencers such as Oxford Nanopore's MinION enable real-time applications in both clinical and environmental health, e.g., detection of bacterial outbreaks. However, there is a bottleneck in the downstream analytics when bioinformatics pipelines are unavailable, e.g., when cloud processing is unreachable due to absence of Internet connection, or only low-end computing devices can be carried on site. For instance, metagenomics classifiers usually require a large amount of memory or specific operating systems/libraries. In this work, we present a platform-friendly software for portable metagenomic analysis of Nanopore data, the Oligomer-based Classifier of Taxonomic Operational and Pan-genome Units via Singletons (OCTOPUS). OCTOPUS is written in Java, reimplements several features of the popular Kraken2 and KrakenUniq software, with original components for improving metagenomics classification on incomplete/sampled reference databases (e.g., selection of bacteria of public health priority), making it ideal for running on smartphones or tablets. We indexed both OCTOPUS and Kraken2 on a bacterial database with ~4,000 reference genomes, then simulated a positive (bacterial genomes from the same species, but different genomes) and two negative (viral, mammalian) Nanopore test sets. On the bacterial test set OCTOPUS yielded sensitivity and precision comparable to Kraken2 (94.4% and 99.8% versus 94.5% and 99.1%, respectively). On non-bacterial sequences (mammals and viral), OCTOPUS dramatically decreased (4- to 16-fold) the false positive rate when compared to Kraken2 (2.1% and 0.7% versus 8.2% and 11.2%, respectively). We also developed customized databases including viruses, and the World Health Organization's set of bacteria of concern for drug resistance, tested with real Nanopore data on an Android smartphone. OCTOPUS is publicly available at https://github.com/DataIntellSystLab/OCTOPUS and https://github.com/Ruiz-HCI-Lab/OctopusMobile.
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The current study aimed to examine the prevalence of and risk factors for cancer and pre-cancerous conditions, comparing transgender and cisgender individuals, using 2012-2023 electronic health record data from a large healthcare system. We identified 2,745 transgender individuals using a previously validated computable phenotype and 54,900 matched cisgender individuals. We calculated the prevalence of cancer and pre-cancer related to human papillomavirus (HPV), human immunodeficiency virus (HIV), tobacco, alcohol, lung, breast, colorectum, and built multivariable logistic models to examine the association between gender identity and the presence of cancer or pre-cancer. Results indicated similar odds of developing cancer across gender identities, but transgender individuals exhibited significantly higher risks for pre-cancerous conditions, including alcohol-related, breast, and colorectal pre-cancers compared to cisgender women, and HPV-related, tobacco-related, alcohol-related, and colorectal pre-cancers compared to cisgender men. These findings underscore the need for tailored interventions and policies addressing cancer health disparities affecting the transgender population.
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BACKGROUND: Racial/ethnic disparities in the HIV care continuum have been well documented in the US, with especially striking inequalities in viral suppression rates between White and Black persons with HIV (PWH). The South is considered an epicenter of the HIV epidemic in the US, with the largest population of PWH living in Florida. It is unclear whether any disparities in viral suppression or immune reconstitution-a clinical outcome highly correlated with overall prognosis-have changed over time or are homogenous geographically. In this analysis, we 1) investigate longitudinal trends in viral suppression and immune reconstitution among PWH in Florida, 2) examine the impact of socio-ecological factors on the association between race/ethnicity and clinical outcomes, 3) explore spatial and temporal variations in disparities in clinical outcomes. METHODS: Data were obtained from the Florida Department of Health for 42,369 PWH enrolled in the Ryan White program during 2008-2020. We linked the data to county-level socio-ecological variables available from County Health Rankings. GEE models were fit to assess the effect of race/ethnicity on immune reconstitution and viral suppression longitudinally. Poisson Bayesian hierarchical models were fit to analyze geographic variations in racial/ethnic disparities while adjusting for socio-ecological factors. RESULTS: Proportions of PWH who experienced viral suppression and immune reconstitution rose by 60% and 45%, respectively, from 2008-2020. Odds of immune reconstitution and viral suppression were significantly higher among White [odds ratio =2.34, 95% credible interval=2.14-2.56; 1.95 (1.85-2.05)], and Hispanic [1.70 (1.54-1.87); 2.18(2.07-2.31)] PWH, compared with Black PWH. These findings remained unchanged after accounting for socio-ecological factors. Rural and urban counties in north-central Florida saw the largest racial/ethnic disparities. CONCLUSIONS: There is persistent, spatially heterogeneous, racial/ethnic disparity in HIV clinical outcomes in Florida. This disparity could not be explained by socio-ecological factors, suggesting that further research on modifiable factors that can improve HIV outcomes among Black and Hispanic PWH in Florida is needed.
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Etnicidade , Infecções por HIV , Humanos , Teorema de Bayes , Florida/epidemiologia , Disparidades em Assistência à Saúde , Hispânico ou Latino , Infecções por HIV/epidemiologia , Brancos , Negro ou Afro-AmericanoRESUMO
Substance use disorder (SUD), a common comorbidity among people with HIV (PWH), adversely affects HIV clinical outcomes and HIV-related comorbidities. However, less is known about the incidence of different chronic conditions, changes in overall comorbidity burden, and health care utilization by SUD status and patterns among PWH in Florida, an area disproportionately affected by the HIV epidemic. We used electronic health records (EHR) from a large southeastern US consortium, the OneFlorida + clinical research data network. We identified a cohort of PWH with 3 + years of EHRs after the first visit with HIV diagnosis. International Classification of Diseases (ICD) codes were used to identify SUD and comorbidity conditions listed in the Charlson comorbidity index (CCI). A total of 42,271 PWH were included (mean age 44.5, 52% Black, 45% female). The prevalence SUD among PWH was 45.1%. Having a SUD diagnosis among PWH was associated with a higher incidence for most of the conditions listed on the CCI and faster increase in CCI score overtime (rate ratio = 1.45, 95%CI 1.42, 1.49). SUD in PWH was associated with a higher mean number of any care visits (21.7 vs. 14.8) and more frequent emergency department (ED, 3.5 vs. 2.0) and inpatient (8.5 vs. 24.5) visits compared to those without SUD. SUD among PWH was associated with a higher comorbidity burden and more frequent ED and inpatient visits than PWH without a diagnosis of SUD. The high SUD prevalence and comorbidity burden call for improved SUD screening, treatment, and integrated care among PWH.
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Comorbidade , Infecções por HIV , Aceitação pelo Paciente de Cuidados de Saúde , Transtornos Relacionados ao Uso de Substâncias , Humanos , Feminino , Florida/epidemiologia , Masculino , Infecções por HIV/epidemiologia , Adulto , Transtornos Relacionados ao Uso de Substâncias/epidemiologia , Pessoa de Meia-Idade , Aceitação pelo Paciente de Cuidados de Saúde/estatística & dados numéricos , Prevalência , Incidência , Registros Eletrônicos de Saúde , Efeitos Psicossociais da DoençaRESUMO
Florida is one of the HIV epicenters with high incidence and marked sociodemographic disparities. We analyzed a decade of statewide electronic health record/claims data-OneFlorida+-to identify and characterize pre-exposure prophylaxis (PrEP) recipients and newly diagnosed HIV cases in Florida. Refined computable phenotype algorithms were applied and a total of 2186 PrEP recipients and 7305 new HIV diagnoses were identified between January 2013 and April 2021. We examined patients' sociodemographic characteristics, stratified by self-reported sex, along with both frequency-driven and expert-selected descriptions of clinical conditions documented within 12 months before the first PrEP use or HIV diagnosis. PrEP utilization rate increased in both sexes; higher rates were observed among males with sex differences widening in recent years. HIV incidence peaked in 2016 and then decreased with minimal sex differences observed. Clinical characteristics were similar between the PrEP and new HIV diagnosis cohorts, characterized by a low prevalence of sexually transmitted infections (STIs) and a high prevalence of mental health and substance use conditions. Study limitations include the overrepresentation of Medicaid recipients, with over 96% of female PrEP users on Medicaid, and the inclusion of those engaged in regular health care. Although PrEP uptake increased in Florida, and HIV incidence decreased, sex disparity among PrEP recipients remained. Screening efforts beyond individuals with documented prior STI and high-risk behavior, especially for females, including integration of mental health care with HIV counseling and testing, are crucial to further equalize PrEP access and improve HIV prevention programs.
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Infecções por HIV , Profilaxia Pré-Exposição , Estados Unidos , Humanos , Feminino , Masculino , Florida/epidemiologia , Registros Eletrônicos de Saúde , Infecções por HIV/diagnóstico , Infecções por HIV/epidemiologia , Infecções por HIV/prevenção & controle , DemografiaRESUMO
The benefits and harms of lung cancer screening (LCS) for patients in the real-world clinical setting have been argued. Recently, discriminative prediction modeling of lung cancer with stratified risk factors has been developed to investigate the real-world effectiveness of LCS from observational data. However, most of these studies were conducted at the population level that only measured the difference in the average outcome between groups. In this study, we built counterfactual prediction models for lung cancer risk and mortality and examined for individual patients whether LCS as a hypothetical intervention reduces lung cancer risk and subsequent mortality. We investigated traditional and deep learning (DL)-based causal methods that provide individualized treatment effect (ITE) at the patient level and evaluated them with a cohort from the OneFlorida+ Clinical Research Consortium. We further discussed and demonstrated that the ITE estimation model can be used to personalize clinical decision support for a broader population.
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Aprendizado Profundo , Neoplasias Pulmonares , Humanos , Detecção Precoce de Câncer , Neoplasias Pulmonares/diagnóstico , Fatores de RiscoRESUMO
BACKGROUND: The rapid evolution of artificial intelligence (AI) in conjunction with recent updates in dual antiplatelet therapy (DAPT) management guidelines emphasizes the necessity for innovative models to predict ischemic or bleeding events after drug-eluting stent implantation. Leveraging AI for dynamic prediction has the potential to revolutionize risk stratification and provide personalized decision support for DAPT management. METHODS AND RESULTS: We developed and validated a new AI-based pipeline using retrospective data of drug-eluting stent-treated patients, sourced from the Cerner Health Facts data set (n=98 236) and Optum's de-identified Clinformatics Data Mart Database (n=9978). The 36 months following drug-eluting stent implantation were designated as our primary forecasting interval, further segmented into 6 sequential prediction windows. We evaluated 5 distinct AI algorithms for their precision in predicting ischemic and bleeding risks. Model discriminative accuracy was assessed using the area under the receiver operating characteristic curve, among other metrics. The weighted light gradient boosting machine stood out as the preeminent model, thus earning its place as our AI-DAPT model. The AI-DAPT demonstrated peak accuracy in the 30 to 36 months window, charting an area under the receiver operating characteristic curve of 90% [95% CI, 88%-92%] for ischemia and 84% [95% CI, 82%-87%] for bleeding predictions. CONCLUSIONS: Our AI-DAPT excels in formulating iterative, refined dynamic predictions by assimilating ongoing updates from patients' clinical profiles, holding value as a novel smart clinical tool to facilitate optimal DAPT duration management with high accuracy and adaptability.
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Doença da Artéria Coronariana , Stents Farmacológicos , Infarto do Miocárdio , Intervenção Coronária Percutânea , Humanos , Inibidores da Agregação Plaquetária/efeitos adversos , Infarto do Miocárdio/etiologia , Doença da Artéria Coronariana/diagnóstico , Doença da Artéria Coronariana/cirurgia , Stents Farmacológicos/efeitos adversos , Inteligência Artificial , Estudos Retrospectivos , Resultado do Tratamento , Fatores de Risco , Quimioterapia Combinada , Hemorragia/induzido quimicamente , Prognóstico , Intervenção Coronária Percutânea/efeitos adversosRESUMO
HIV-related stigma is a key contributor to poor HIV-related health outcomes. The purpose of this study is to explore implementing a stigma measure into routine HIV care focusing on the 10-item Medical Monitoring Project measure as a proposed measure. Healthcare providers engaged in HIV-related care in Florida were recruited. Participants completed an interview about their perceptions of measures to assess stigma during clinical care. The analysis followed a directed content approach. Fifteen participants completed the interviews (87% female, 47% non-Hispanic White, case manager 40%). Most providers thought that talking about stigma would be helpful (89%). Three major themes emerged from the analysis: acceptability, subscales of interest, and utility. In acceptability, participants mentioned that assessing stigma could encourage patient-centered care and serve as a conversation starter, but some mentioned not having enough time. Participants thought that the disclosure concerns and negative self-image subscales were most relevant. Some worried they would not have resources for patients or that some issues were beyond their influence. Participants were generally supportive of routinely addressing HIV-related stigma in clinical care, but were concerned that resources, especially to address concerns about disclosure and negative self-image, were not available.
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Infecções por HIV , Humanos , Feminino , Masculino , Florida , Estigma Social , Ansiedade , RevelaçãoRESUMO
The coronavirus disease of 2019 (COVID-19) pandemic is characterized by sequential emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and lineages outcompeting previously circulating ones because of, among other factors, increased transmissibility and immune escape1-3. We devised an unsupervised deep learning AutoEncoder for viral genomes anomaly detection to predict future dominant lineages (FDLs), i.e., lineages or sublineages comprising ≥10% of viral sequences added to the GISAID database on a given week4. The algorithm was trained and validated by assembling global and country-specific data sets from 16,187,950 Spike protein sequences sampled between December 24th, 2019, and November 8th, 2023. The AutoEncoder flags low frequency FDLs (0.01% - 3%), with median lead times of 4-16 weeks. Over time, positive predictive values oscillate, decreasing linearly with the number of unique sequences per data set, showing average performance up to 30 times better than baseline approaches. The B.1.617.2 vaccine reference strain was flagged as FDL when its frequency was only 0.01%, more than one year earlier of being considered for an updated COVID-19 vaccine. Our AutoEncoder, applicable in principle to any pathogen, also pinpoints specific mutations potentially linked to increased fitness, and may provide significant insights for the optimization of public health pre-emptive intervention strategies.
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This study quantifies health outcome disparities in invasive Methicillin-Resistant Staphylococcus aureus (MRSA) infections by leveraging a novel artificial intelligence (AI) fairness algorithm, the Fairness-Aware Causal paThs (FACTS) decomposition, and applying it to real-world electronic health record (EHR) data. We spatiotemporally linked 9 years of EHRs from a large healthcare provider in Florida, USA, with contextual social determinants of health (SDoH). We first created a causal structure graph connecting SDoH with individual clinical measurements before/upon diagnosis of invasive MRSA infection, treatments, side effects, and outcomes; then, we applied FACTS to quantify outcome potential disparities of different causal pathways including SDoH, clinical and demographic variables. We found moderate disparity with respect to demographics and SDoH, and all the top ranked pathways that led to outcome disparities in age, gender, race, and income, included comorbidity. Prior kidney impairment, vancomycin use, and timing were associated with racial disparity, while income, rurality, and available healthcare facilities contributed to gender disparity. From an intervention standpoint, our results highlight the necessity of devising policies that consider both clinical factors and SDoH. In conclusion, this work demonstrates a practical utility of fairness AI methods in public health settings.
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Infecções Comunitárias Adquiridas , Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Humanos , Infecções Estafilocócicas/tratamento farmacológico , Infecções Estafilocócicas/diagnóstico , Inteligência Artificial , Infecções Comunitárias Adquiridas/tratamento farmacológico , Biologia Computacional , Algoritmos , Avaliação de Resultados em Cuidados de Saúde , Antibacterianos/uso terapêuticoRESUMO
BACKGROUND: Hospital-induced delirium is one of the most common and costly iatrogenic conditions, and its incidence is predicted to increase as the population of the United States ages. An academic and clinical interdisciplinary systems approach is needed to reduce the frequency and impact of hospital-induced delirium. OBJECTIVE: The long-term goal of our research is to enhance the safety of hospitalized older adults by reducing iatrogenic conditions through an effective learning health system. In this study, we will develop models for predicting hospital-induced delirium. In order to accomplish this objective, we will create a computable phenotype for our outcome (hospital-induced delirium), design an expert-based traditional logistic regression model, leverage machine learning techniques to generate a model using structured data, and use machine learning and natural language processing to produce an integrated model with components from both structured data and text data. METHODS: This study will explore text-based data, such as nursing notes, to improve the predictive capability of prognostic models for hospital-induced delirium. By using supervised and unsupervised text mining in addition to structured data, we will examine multiple types of information in electronic health record data to predict medical-surgical patient risk of developing delirium. Development and validation will be compliant to the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD) statement. RESULTS: Work on this project will take place through March 2024. For this study, we will use data from approximately 332,230 encounters that occurred between January 2012 to May 2021. Findings from this project will be disseminated at scientific conferences and in peer-reviewed journals. CONCLUSIONS: Success in this study will yield a durable, high-performing research-data infrastructure that will process, extract, and analyze clinical text data in near real time. This model has the potential to be integrated into the electronic health record and provide point-of-care decision support to prevent harm and improve quality of care. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/48521.
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OBJECTIVE: Having sufficient population coverage from the electronic health records (EHRs)-connected health system is essential for building a comprehensive EHR-based diabetes surveillance system. This study aimed to establish an EHR-based type 1 diabetes (T1D) surveillance system for children and adolescents across racial and ethnic groups by identifying the minimum population coverage from EHR-connected health systems to accurately estimate T1D prevalence. MATERIALS AND METHODS: We conducted a retrospective, cross-sectional analysis involving children and adolescents <20 years old identified from the OneFlorida+ Clinical Research Network (2018-2020). T1D cases were identified using a previously validated computable phenotyping algorithm. The T1D prevalence for each ZIP Code Tabulation Area (ZCTA, 5 digits), defined as the number of T1D cases divided by the total number of residents in the corresponding ZCTA, was calculated. Population coverage for each ZCTA was measured using observed health system penetration rates (HSPR), which was calculated as the ratio of residents in the corresponding ZTCA and captured by OneFlorida+ to the overall population in the same ZCTA reported by the Census. We used a recursive partitioning algorithm to identify the minimum required observed HSPR to estimate T1D prevalence and compare our estimate with the reported T1D prevalence from the SEARCH study. RESULTS: Observed HSPRs of 55%, 55%, and 60% were identified as the minimum thresholds for the non-Hispanic White, non-Hispanic Black, and Hispanic populations. The estimated T1D prevalence for non-Hispanic White and non-Hispanic Black were 2.87 and 2.29 per 1000 youth, which are comparable to the reference study's estimation. The estimated prevalence of T1D for Hispanics (2.76 per 1000 youth) was higher than the reference study's estimation (1.48-1.64 per 1000 youth). The standardized T1D prevalence in the overall Florida population was 2.81 per 1000 youth in 2019. CONCLUSION: Our study provides a method to estimate T1D prevalence in children and adolescents using EHRs and reports the estimated HSPRs and prevalence of T1D for different race and ethnicity groups to facilitate EHR-based diabetes surveillance.
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Diabetes Mellitus Tipo 1 , Criança , Humanos , Adolescente , Adulto Jovem , Adulto , Diabetes Mellitus Tipo 1/epidemiologia , Prevalência , Registros Eletrônicos de Saúde , Estudos Transversais , Estudos RetrospectivosRESUMO
Developing models for individualized, time-varying treatment optimization from observational data with large variable spaces, e.g., electronic health records (EHR), is problematic because of inherent, complex bias that can change over time. Traditional methods such as the g-formula are robust, but must identify critical subsets of variables due to combinatorial issues. Machine learning approaches such as causal survival forests have fewer constraints and can provide fine-tuned, individualized counterfactual predictions. In this study, we aimed to optimize time-varying antibiotic treatment -identifying treatment heterogeneity and conditional treatment effects- against invasive methicillin-resistant Staphylococcus Aureus (MRSA) infections, using statewide EHR data collected in Florida, USA. While many previous studies focused on measuring the effects of the first empiric treatment (i.e., usually vancomycin), our study focuses on dynamic sequential treatment changes, comparing possible vancomycin switches with other antibiotics at clinically relevant time points, e.g., after obtaining a bacterial culture and susceptibility testing. Our study population included adult individuals admitted to the hospital with invasive MRSA. We collected demographic, clinical, medication, and laboratory information from the EHR for these patients. Then, we followed three sequential antibiotic choices (i.e., their empiric treatment, subsequent directed treatment, and final sustaining treatment), evaluating 30-day mortality as the outcome. We applied both causal survival forests and g-formula using different clinical intervention policies. We found that switching from vancomycin to another antibiotic improved survival probability, yet there was a benefit from initiating vancomycin compared to not using it at any time point. These findings show consistency with the empiric choice of vancomycin before confirmation of MRSA and shed light on how to manage switches on course. In conclusion, this application of causal machine learning on EHR demonstrates utility in modeling dynamic, heterogeneous treatment effects that cannot be evaluated precisely using randomized clinical trials.
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BACKGROUND: Prognostic models of hospital-induced delirium, that include potential predisposing and precipitating factors, may be used to identify vulnerable patients and inform the implementation of tailored preventive interventions. It is recommended that, in prediction model development studies, candidate predictors are selected on the basis of existing knowledge, including knowledge from clinical practice. The purpose of this article is to describe the process of identifying and operationalizing candidate predictors of hospital-induced delirium for application in a prediction model development study using a practice-based approach. METHODS: This study is part of a larger, retrospective cohort study that is developing prognostic models of hospital-induced delirium for medical-surgical older adult patients using structured data from administrative and electronic health records. First, we conducted a review of the literature to identify clinical concepts that had been used as candidate predictors in prognostic model development-and-validation studies of hospital-induced delirium. Then, we consulted a multidisciplinary task force of nine members who independently judged whether each clinical concept was associated with hospital-induced delirium. Finally, we mapped the clinical concepts to the administrative and electronic health records and operationalized our candidate predictors. RESULTS: In the review of 34 studies, we identified 504 unique clinical concepts. Two-thirds of the clinical concepts (337/504) were used as candidate predictors only once. The most common clinical concepts included age (31/34), sex (29/34), and alcohol use (22/34). 96% of the clinical concepts (484/504) were judged to be associated with the development of hospital-induced delirium by at least two members of the task force. All of the task force members agreed that 47 or 9% of the 504 clinical concepts were associated with hospital-induced delirium. CONCLUSIONS: Heterogeneity among candidate predictors of hospital-induced delirium in the literature suggests a still evolving list of factors that contribute to the development of this complex phenomenon. We demonstrated a practice-based approach to variable selection for our model development study of hospital-induced delirium. Expert judgement of variables enabled us to categorize the variables based on the amount of agreement among the experts and plan for the development of different models, including an expert-model and data-driven model.
Assuntos
Comitês Consultivos , Delírio , Humanos , Idoso , Estudos Retrospectivos , Consumo de Bebidas Alcoólicas , Hospitais , Delírio/diagnósticoRESUMO
BACKGROUND: Integrase strand transferase inhibitors (INSTI), including raltegravir (RAL), elvitegravir (ELV), and dolutegravir (DTG), have demonstrated better efficacy and tolerability than other combination antiretroviral therapy (cART) classes in clinical trials; however, studies of sustainability of INSTI-containing therapy in the long-term are sparse. The purpose of this study was to provide an epidemiological overview comparing the outcome performance of different INSTI-based regimens longitudinally, including the metrics of efficacy, safety, convenience, and durability among a large, nationally representative cohort of persons living with HIV in Italy. METHODS: We selected subjects in the MaSTER cohort (an Italian multicenter, hospital-based cohort established in the mid-1990s that currently has enrolled over 24,000 PLWH) who initiated an INSTI-based regimen either when naïve or following a regimen switch. Cox proportional hazards regression models were fitted to evaluate associations between therapy interruptions and age, sex, nationality, transmission risk group, viral suppression status, CD4 + T-cell count, diagnosis year, cART status (naïve or experienced), and hepatitis coinfection. Results were stratified by cART INSTI type. RESULTS: There were 8173 participants who initiated an INSTI-based cART regimen in the MaSTER cohort between 2009 and 2017. The population was majority male (72.6%), of Italian nationality (88.6%), and cART-experienced (83.0%). Mean age was 49.7 (standard deviation: 13.9) years. In total, interruptions of the 1st INSTI-based treatment were recorded in 34% of cases. The most frequently cited reason for interruption among all three drug types was safety problems. In the survival analysis, past history of cART use was associated with higher hazards of interruption due to poor efficacy for all three drug types when compared to persons who were cART naïve. Non-viral suppression and CD4 + T-cell count < 200/mm3 at baseline were associated with higher hazards of interruption due to efficacy, safety, and durability reasons. Non-Italian nationality was linked to higher hazards of efficacy interruption for RAL and EVG. Age was negatively associated with interruption due to convenience and positively associated with interruption due to safety reasons. People who injects drugs (PWID) were associated with higher hazards of interruption due to convenience problems. Hepatitis coinfection was linked to higher hazards of interruption due to safety concerns for people receiving RAL. CONCLUSION: One-third of the population experienced an interruption of any drugs included in INSTI therapy in this study. The most frequent reason for interruption was safety concerns which accounted for one-fifth of interruptions among the full study population, mainly switched to DTG. The hazard for interruption was higher for low baseline CD4 + T-cell counts, higher baseline HIV-RNA, non-Italian nationality, older age, PWID and possible co-infections with hepatitis viruses. The risk ratio was higher for past history of cART use compared to persons who were cART naive, use of regimens containing 3 drugs compared to regimens containing 2 drugs. Durability worked in favor of DTG which appeared to perform better in this cohort compared to RAL and EVG, though length of follow-up was significantly shorter for DTG. These observational results need to be confirmed in further perspective studies with longer follow-up.