scholarly journals Supervised Machine Learning Approach to Identify Early Predictors of Poor Outcome in Patients with COVID-19 Presenting to a Large Quaternary Care Hospital in New York City

2021 ◽  
Vol 10 (16) ◽  
pp. 3523
Author(s):  
Jason Zucker ◽  
Angela Gomez-Simmonds ◽  
Lawrence J. Purpura ◽  
Sherif Shoucri ◽  
Elijah LaSota ◽  
...  

Background: The progression of clinical manifestations in patients with coronavirus disease 2019 (COVID-19) highlights the need to account for symptom duration at the time of hospital presentation in decision-making algorithms. Methods: We performed a nested case–control analysis of 4103 adult patients with COVID-19 and at least 28 days of follow-up who presented to a New York City medical center. Multivariable logistic regression and classification and regression tree (CART) analysis were used to identify predictors of poor outcome. Results: Patients presenting to the hospital earlier in their disease course were older, had more comorbidities, and a greater proportion decompensated (<4 days, 41%; 4–8 days, 31%; >8 days, 26%). The first recorded oxygen delivery method was the most important predictor of decompensation overall in CART analysis. In patients with symptoms for <4, 4–8, and >8 days, requiring at least non-rebreather, age ≥ 63 years, and neutrophil/lymphocyte ratio ≥ 5.1; requiring at least non-rebreather, IL-6 ≥ 24.7 pg/mL, and D-dimer ≥ 2.4 µg/mL; and IL-6 ≥ 64.3 pg/mL, requiring non-rebreather, and CRP ≥ 152.5 mg/mL in predictive models were independently associated with poor outcome, respectively. Conclusion: Symptom duration in tandem with initial clinical and laboratory markers can be used to identify patients with COVID-19 at increased risk for poor outcomes.

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S99-S99
Author(s):  
Chaorui Huang ◽  
David Lucero ◽  
Denise Paone ◽  
Ellenie Tuazon ◽  
Demetre Daskalakis

Abstract Background Along with a growing opioid epidemic nationwide, opioid users often have an increased risk of severe infectious diseases including endocarditis, osteomyelitis, and central nervous system (CNS) abscess. As the largest city in the United States, New York City (NYC) may serve as a study model for opioid use and infectious diseases. We investigated the association between opioid use and hospitalizations for endocarditis, osteomyelitis, and CNS abscess in NYC. Methods Data for NYC residents aged ≥18 years discharged from New York State hospitals during 2001–2014 were analyzed using a hospital discharge dataset. We defined a hospitalization for endocarditis, osteomyelitis, and CNS abscess as one with a principal or secondary diagnosis for these conditions within the discharge record. We identified opioid users by examining principal or secondary diagnoses for opioid use within the discharge record at the time of hospitalization for endocarditis, osteomyelitis, and CNS abscess. Log-binomial model was applied among all hospitalized patients using endocarditis, osteomyelitis, and CNS abscess as the outcome, adjusting for age, sex, race, and borough. Results During 2001–2014, there were 139,392 hospitalizations in total for endocarditis, osteomyelitis, or CNS abscess, of which 8,823 (6.3%) were among opioid users. There was an increased risk of hospitalization for endocarditis [RR: 2.6 (95% CI: 2.5–2.7)], osteomyelitis [RR: 1.1 (95% CI: 1.1–1.1)], and CNS abscesses [RR: 1.9 (95% CI: 1.8–2.1)] among hospitalized opioid users compared with hospitalized nonopioid users, adjusted by age, sex, race, and borough. Hospitalized opioid users had four times the risk for endocarditis hospitalization compared with hospitalized nonopioid users in the 18–44 year age group (RR: 4.2 [95% CI: 3.9–4.5]) (Table 1). Conclusion These results provide further evidence that opioid use is associated with an increased risk of endocarditis, osteomyelitis, and CNS abscess. Efforts to combat the opioid epidemic might lower the overall incidence of endocarditis, osteomyelitis, and CNS abscess. Disclosures All authors: No reported disclosures.


Author(s):  
Angela Gomez-Simmonds ◽  
Medini K Annavajhala ◽  
Thomas H McConville ◽  
Donald E Dietz ◽  
Sherif M Shoucri ◽  
...  

Abstract Background Patients with COVID-19 may be at increased risk for secondary bacterial infections with MDR pathogens, including carbapenemase-producing Enterobacterales (CPE). Objectives We sought to rapidly investigate the clinical characteristics, population structure and mechanisms of resistance of CPE causing secondary infections in patients with COVID-19. Methods We retrospectively identified CPE clinical isolates collected from patients testing positive for SARS-CoV-2 between March and April 2020 at our medical centre in New York City. Available isolates underwent nanopore sequencing for rapid genotyping, antibiotic resistance gene detection and phylogenetic analysis. Results We identified 31 CPE isolates from 13 patients, including 27 Klebsiella pneumoniae and 4 Enterobacter cloacae complex isolates. Most patients (11/13) had a positive respiratory culture and 7/13 developed bacteraemia; treatment failure was common. Twenty isolates were available for WGS. Most K. pneumoniae (16/17) belonged to ST258 and encoded KPC (15 KPC-2; 1 KPC-3); one ST70 isolate encoded KPC-2. E. cloacae isolates belonged to ST270 and encoded NDM-1. Nanopore sequencing enabled identification of at least four distinct ST258 lineages in COVID-19 patients, which were validated by Illumina sequencing data. Conclusions While CPE prevalence has declined substantially in New York City in recent years, increased detection in patients with COVID-19 may signal a re-emergence of these highly resistant pathogens in the wake of the global pandemic. Increased surveillance and antimicrobial stewardship efforts, as well as identification of optimal treatment approaches for CPE, will be needed to mitigate their future impact.


2021 ◽  
Vol 8 ◽  
Author(s):  
Annie Wang ◽  
Stephanie H. Chang ◽  
Eric J. Kim ◽  
Jamie L. Bessich ◽  
Joshua K. Sabari ◽  
...  

Management of patients with lung cancer continues to be challenging during the COVID-19 pandemic, due to the increased risk of complications in this subset of patients. During the COVID-19 surge in New York City, New York University Langone Health adopted triage strategies to help with care for lung cancer patients, with good surgical outcomes and no transmission of COVID-19 to patients or healthcare workers. Here, we will review current recommendations regarding screening and management of lung cancer patients during both a non-surge phase and surge phase of COVID-19.


Urban Studies ◽  
2021 ◽  
pp. 004209802110443
Author(s):  
Gayatri Kawlra ◽  
Kazuki Sakamoto

This paper examines how fragmentation of critical infrastructure impacts the spread of the coronavirus outbreak in New York City at the neighbourhood level. The location of transportation hubs, grocery stores, pharmacies, hospitals and parks plays an important role in shaping spatial disparities in virus spread. Using supervised machine learning and spatial regression modelling we examine how the geography of COVID-19 case rates is influenced by the spatial arrangement of four critical sectors of the built environment during the public health emergency in New York City: health care facilities, mobility networks, food and nutrition and open space. Our models suggest that an analysis of urban health vulnerability is incomplete without the inclusion of critical infrastructure metrics in dense urban geographies. Our findings show that COVID-19 risk at the zip code level is influenced by (1) socio-demographic vulnerability, (2) epidemiological risk, and (3) availability and access to critical infrastructure.


2008 ◽  
Vol 35 (9) ◽  
pp. 814-817 ◽  
Author(s):  
Christy M. McKinney ◽  
Ellen J. Klingler ◽  
Rachel Paneth-Pollak ◽  
Julia A. Schillinger ◽  
R Charon Gwynn ◽  
...  

2020 ◽  
pp. 1429-1444
Author(s):  
Rachel E. Rosenblum ◽  
Celina Ang ◽  
Sabrina A. Suckiel ◽  
Emily R. Soper ◽  
Meenakshi R. Sigireddi ◽  
...  

PURPOSE Limited data are available on the prevalence and clinical impact of Lynch syndrome (LS)–associated genomic variants in non-European ancestry populations. We identified and characterized individuals harboring LS-associated variants in the ancestrally diverse Bio Me Biobank in New York City. PATIENTS AND METHODS Exome sequence data from 30,223 adult Bio Me participants were evaluated for pathogenic, likely pathogenic, and predicted loss-of-function variants in MLH1, MSH2, MSH6, and PMS2. Survey and electronic health record data from variant-positive individuals were reviewed for personal and family cancer histories. RESULTS We identified 70 individuals (0.2%) harboring LS-associated variants in MLH1 (n = 12; 17%), MSH2 (n = 13; 19%), MSH6 (n = 16; 23%), and PMS2 (n = 29; 41%). The overall prevalence was 1 in 432, with higher prevalence among individuals of self-reported African ancestry (1 in 299) than among Hispanic/Latinx (1 in 654) or European (1 in 518) ancestries. Thirteen variant-positive individuals (19%) had a personal history, and 19 (27%) had a family history of an LS-related cancer. LS-related cancer rates were highest in individuals with MSH6 variants (31%) and lowest in those with PMS2 variants (7%). LS-associated variants were associated with increased risk of colorectal (odds ratio [OR], 5.0; P = .02) and endometrial (OR, 30.1; P = 8.5 × 10−9) cancers in Bio Me. Only 2 variant-positive individuals (3%) had a documented diagnosis of LS. CONCLUSION We found a higher prevalence of LS-associated variants among individuals of African ancestry in New York City. Although cancer risk is significantly increased among variant-positive individuals, the majority do not harbor a clinical diagnosis of LS, suggesting underrecognition of this disease.


2015 ◽  
Vol 53 (7) ◽  
pp. 2060-2067 ◽  
Author(s):  
Angela Gomez-Simmonds ◽  
Michelle Greenman ◽  
Sean B. Sullivan ◽  
Joshua P. Tanner ◽  
Madeleine G. Sowash ◽  
...  

Despite the growing importance of carbapenem-resistantKlebsiella pneumoniae(CRKP), the clonal relationships between CRKP and antibiotic-susceptible isolates remain unclear. We compared the genetic diversity and clinical features of CRKP, third-generation and/or fourth-generation cephalosporin-resistant (Ceph-R)K. pneumoniae, and susceptibleK. pneumoniaeisolates causing bloodstream infections at a tertiary care hospital in New York City between January 2012 and July 2013. Drug susceptibilities were determined with the Vitek 2 system. Isolates underwent multilocus sequence typing and PCR sequencing of thewziandblaKPCgenes. Clinical and microbiological data were extracted from patient records and correlated with molecular data. Among 223 patients, we identified 272 isolates. Of these, 194 were susceptible, 30 Ceph-R, and 48 CRKP, belonging to 144 sequence types (STs). Susceptible (127 STs) and Ceph-R (20 STs) isolates were highly diverse. ST258 dominated CRKP strains (12 STs, with 63% ST258). There was minimal overlap in STs between resistance groups. TheblaKPC-3gene (30%) was restricted to ST258/wzi154, whereasblaKPC-2(70%) was observed for severalwziallele types. CRKP infections occurred more frequently among solid organ transplant (31%) and dialysis (17%) patients. Mortality rates were high overall (28%) and highest among CRKP-infected patients (59%). In multivariable analyses, advanced age, comorbidities, and disease severity were significant predictors of 30-day mortality rates, whereas theK. pneumoniaesusceptibility phenotype was not. Among CRKP infections, we observed a borderline significant association of increased mortality rates with ST258 and thewzi154 allele. Although the clonal spread of ST258 continues to contribute substantially to the dissemination of CRKP, non-ST258 strains appear to be evolving. Further investigations into the mechanisms promoting CRKP diversification and the effects of clonal backgrounds on outcomes are warranted.


2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S114-S114
Author(s):  
T Sherpa ◽  
T Choesang ◽  
S Ahmad ◽  
F M Huq Ronny

Abstract Introduction/Objective Operated under different acute care hospital clinical laboratory limited-service laboratory (LSL) licenses, our New York City five borough spanning multisite ambulatory clinics and school-based clinics have been offering various waived point-of-care tests (POCTs) and provider-performed microscopy (PPM) to the local communities. A wide range of variability existed among the clinics concerning regulatory compliance, test performance, quality control and training. To ensure standardization and quality of POCT across the health system, our laboratory service adopted and implemented a plan for systemwide LSL transfer from the acute care hospitals to ambulatory care laboratory service for centralized implementation, monitoring, and oversight of the POCT operations. Methods/Case Report Having over 60 clinics, while transferring the LSLs, we chose multi-site license with ten or more sites on each license and by phase transfer from NYSDOH. Since the commencement of the transfer, system wide our qualified laboratory personnel have been updating and providing standard operating procedures (SOP), performing quality assurance and validation of new tests/devices, providing competency assessments and helping clinical staffs maintain compliance with state and other regulatory agencies. Results (if a Case Study enter NA) After the final phase of the transfer and POCT standardization implementation in 63 clinics, currently the clinical staffs performing POCT, get expeditious training and troubleshooting in more timely manner and the providers get the results of the ordered POCTs much faster and more efficiently and overall the quality metrics get improved markedly, indicated by internal audit team. Conclusion Even though Implementation of the planned POCT standardization was initially challenging due to the vastness and complexity of our multisite ambulatory care network and later confounded by the COVID -19 pandemic effect but eventually, it helped improve patient care delivery significantly and very effectively. Expectedly, our planned transfer implementation provided standardization and ensured improved quality of POC testing across our health system.


2017 ◽  
Vol 1 (S1) ◽  
pp. 23-23
Author(s):  
Christina Pressl ◽  
Caroline Jiang ◽  
Joel Correa da Rosa ◽  
Maximilian Friedrich ◽  
Winrich Freiwald ◽  
...  

OBJECTIVES/SPECIFIC AIMS: We aim to examine the epidemiological characteristics of prosopagnosia by querying and analyzing a large deidentified clinical data set from 12 New York City-based hospitals and Federally Qualified Health Centers (FQHCs). The PCORI-funded New York City Clinical Data Research Network (NYC-CDRN) contains ~4.5 million deidentified ICD-coded electronic health records (EHRs) with comprehensive longitudinal information on demographics, patient visits, clinical conditions/diagnoses, laboratory and radiology results, medications, and clinical procedures. The NYC-CDRN will be expanded to include other data sources, including insurance claims, social determinant of health, patient reported outcomes, and patient generated data. The central hypothesis was that systematic mining of this database would reveal new epidemiological information about prosopagnosia. We developed a computable phenotype for prosopagnosia, using the International Classification of Diseases version 9 (ICD-9). The computable phenotype consisted of the diagnostic code for the condition under study, prosopagnosia (ICD-9 code 368.16), as well as the codes for known surrogate diagnoses. We expected to identify cases of acquired prosopagnosia, where the condition occurs only after brain damage, due to stroke, trauma, or meningitis for example, and cases of developmental prosopagnosia, where the condition is present from an early age, with no history of brain damage. The goals of this project were to provide new information about the condition’s prevalence rate in the New York City area, which could be furthermore translated into wider geographical areas and to yield novel details about its antecedents and comorbid conditions. METHODS/STUDY POPULATION: To determine the presence of the diagnosis of interest, prosopagnosia, and common co-occurring conditions among a New York City-based study population, we investigated a large database in collaboration with the NYC-CDRN. At the time the large database was mined it contained ~4 million ICD-9 coded EHRs. We first created a search paradigm; applicable for screening the database that consists of ICD-9 coded EHRs. We generated a list of ICD-9 codes indicative for the patients’ difficulties with the perception of faces (368.16), which indicates the presence of the condition as part of the psychophysical visual disturbances complex, and this code identified 871 patients. Furthermore, we collected codes that indicate the presence of conditions that are known to be surrogate diagnoses of prosopagnosia. ICD-9 codes for surrogate diagnoses included for example, 854.* (coding for personal history of traumatic brain injury, n=1,409), 434.01, 434.11, and 434.91 (coding for cerebral thrombosis, embolus and artery occlusion unspecified with cerebral infarction, n=19,409), and 191.2 (coding for malignant neoplasm of the temporal lobe, n=566). In October 2015, coding was changed to the new ICD-10 coding system. No additional patients were revealed from the data set when the cohort was searched for the presence of corresponding ICD-10 codes, as institutions are currently in transition from ICD-9 to ICD-10. Using this search query with the large database, we extracted novel information about the epidemiological and demographical distribution of prosopagnosia and furthermore, gained new knowledge about commonly associated diseases. The fact that it must be presumed that the majority of diagnoses of prosopagnosia have been made on the basis of patients’ self-reports and clinicians’ judgments represents a limiting factor in this study. We are currently exploring machine-learning strategies to identify potential false-negative cases among the patients with surrogate diagnoses. RESULTS/ANTICIPATED RESULTS: Investigations and application of our search query revealed a total number of n=129,549 patients carrying either the diagnosis code for prosopagnosia or the codes for the known surrogate diagnoses. There were 871 patients who carried the ICD-9 code 368.16, indicating the potential presence of prosopagnosia among other visual disturbances. Remaining patients (n=128,678) carried codes for known surrogate diagnoses, contained in the search query. Statistical analyses revealed elevated odds ratios for men (OR=1.55, 95% CI: 1.36, 1.77, p<0.0001), and for Black/African Americans Versus White individuals (OR=2.09, 95% CI: 1.74, 2.51, p<0.0001). DISCUSSION/SIGNIFICANCE OF IMPACT: Currently, the prevalence of prosopagnosia remains unknown. Face blind individuals are struggling to recognize their social contacts by their face only in every day life and are therefore prone to experience reduced quality of life. We searched the large NYC-based clinical database, containing more than 4.5 million deidentified ICD-coded health records, for cases of prosopagnosia to shed light into its prevalence and epidemiological characteristics. We furthermore, mined the database for cases carrying known surrogate diagnoses to explore the magnitude and characteristics of individuals potentially under increased risk. Our efforts address a great healthcare need, as they revealed new epidemiological knowledge of a vulnerable and understudied population. The results of this project reveal new insights into the epidemiological characteristics of prosopagnosia and its surrogate diagnoses, and demonstrate the feasibility of mining large clinical databases to identify rare clinical populations. Our results suggest the need for a more targeted diagnostic assessment of face perception abilities in populations under increased risk.


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