bluuebunny/crossref_metadata_2025_split huggingface dataset:
271. Determining Risk Factors Associated with an Increased Incidence of Pulmonary Embolism: A Multi-Center Study of 3,675 Patients
Authors: Wang Lucas , Abualfoul Mujahed , Aten Kristopher , Azimi Ariella , Canela Victor , Hoang Lawrence , Prathivada Sri , Vu Michael , Zhao Sherry , Sidhu Manavjot 
Published: December 2022

Abstract

Background
Coronavirus Disease 2019 (COVID-19) is associated with an increased incidence of pulmonary embolism (PE). Both conditions increase hospital complications and mortality, especially when exhibited concurrently. Unfortunately, both conditions may present similarly, and physicians often have a difficult time finding clinical indicators to suggest pursuing further evaluation of a PE during a COVID-19 infection.

Methods
Using a multi-center facility database, we conducted a retrospective analysis of 3,675 COVID-19 patients at Methodist Health System from March 2020 to December 2020. COVID-19 infection was determined via molecular PCR testing and PE was determined by computed tomography (CT) scan with angiography. Patient demographics and laboratory values were determined by a manual review of patient charts. Chi-Square test was used to analyze observed variables. Odds ratios were calculated for variables with a statistically significant difference (p &lt; 0.05).

Results
Of the 3,675 patients diagnosed with COVID-19, 150 (4.1%) were diagnosed with PE. Elevated D-dimer level had a statistically significant association with increased rate of PE (OR 0.1988, 95% CI 0.0727 – 0.5438, p &lt; 0.001). Factors such as elevated C-reactive protein (p = 0.61), IL-6 (p = 0.26), smoking history (p = 0.70), age over 65 (p=0.54), BMI over 25 (p = 0.42), and history of chronic kidney disease (p = 0.16) did not show a significant association with PE incidence. Of note, patients with PE during admission were seen to have an increased incidence of intubation (OR 0.40, 95% CI 0.2660 – 0.6029, p &lt; 0.001).

Conclusion
Our study suggests that COVID-19 patients with elevated D-dimer have higher odds of having a PE. This study also suggests that COVID-19 patients that develop a PE during hospitalization are more likely to require intubation.

Disclosures
All Authors: No reported disclosures.
275. Evaluating the COVID-19 Pandemic in US Veterans: Transitioning from Delta to Omicron Variants
Authors: Lier Audun J , Lobo Zeena , Psevdos George 
Published: December 2022

Abstract

Background
During the COVID-19 pandemic many new variants of the SARS-CoV-2 virus have evolved. The omicron variant is the latest of concern and has numerous mutations in the spike protein (SP) which may alter COVID19 vaccine and therapeutic efficacy. We assessed whether COVID19 vaccination status would be protective among US Veterans (USV) who were diagnosed with SARS-CoV2 infection and performed an epidemiological analysis of this cohort.

Methods
A retrospective chart review was performed of USV with PCR confirmed SARS-CoV-2 infection who presented to Northport Veterans Affairs Medical Center between 11/1/2021 and 4/15/2022. Demographic information, vaccine status, medical comorbidities, SARS-CoV2 infection history, medical therapy receipt, need for hospitalization, SARS-COV-2 sequencing, and SP receptor-biding domain (RBD) IgG levels were reviewed. Two sample t-test and Chi-square analyses were performed.

Results
605 USV were diagnosed with SARS-CoV2, median age was 62 years, 559 (92.4%) were male, 474 (78.3%) Caucasian and 77 (12.7%) Hispanic. 426 (70.4%) received at least one COVID19 vaccine dose, largely mRNA (n=400, 66.1%). Median time from vaccine dose to SARS-CoV2 diagnosis was 211 days (1-468). 26 (4.3%) USV had a previous history of SARS-CoV2 infection and 38 vaccinated USV had RBD-SP IgG titers (positive &gt; 1 S/CO) at time of presentation, median 6.8 S/CO (0.06 to 71.21). Unvaccinated USV had a higher mean body mass index (31.0 vs. 30.0, p=0.04), and more commonly carried a diagnosis of COPD or asthma (20.0 vs. 11.8%, p=0.0005). A greater number of vaccinated USV utilized tobacco (44.2 vs 6.1%, p&lt; 0.0001) or opioids (6.8 vs 1.1%, p&lt; 0.0001). Unvaccinated USV more often required remdesivir (RDV) or dexamethasone (DEX) therapy (10.6 vs 6.6%, p=0.04). There was no difference in hospitalizations, monoclonal antibody use, or all-cause mortality between groups. Omicron BA.1 was first found on December 13, BA.2 on March 9 and final Delta variant on January 12.
Demographic characteristics of the entire cohort, as well as by vaccination status
Monthly SARS-CoV2 infections among US Veterans
Monthly infections with delta and omicron SARS-CoV2 variants among vaccinated and unvaccinated US Veterans between 11/1/21 and 4/15/22
Daily SARS-CoV2 infections among US Veterans
Daily infections with delta and omicron SARS-CoV2 variants among vaccinated and unvaccinated US Veterans between 11/1/21 and 4/15/22

Conclusion
Omicron and Delta SARS-CoV-2 infections occurred in both vaccinated and unvaccinated USV, including among vaccinated persons with detectable neutralizing IgG titers. Unvaccinated USV were more likely to utilize RDV and DEX, suggesting severe infection was more common in this group.

Disclosures
All Authors: No reported disclosures.
282. Occurrence of adverse events and factors related to prognosis in a cohort of patients hospitalized with COVID-19 at University hospital - UNICAMP, Brazil.
Authors: Luz Maitê V , Silva Julian F , Ceccato Hugo D , Souza Paulo J , Villar Pedro M E , Mendes Paulo R A , Resende Mariângela R , Pereira Mônica C , Conterno Lucieni O 
Published: December 2022

Abstract

Background
In Brazil, 30.378.061 cases of COVID were reported and 662.866 deaths up to April 27 of 2022. Hospital infections and other hospital adverse events may increase the risk of death in patients with COVID-19.

Methods
Cohort study that included 650 adult patients hospitalized with a diagnosis of SARS CoV-2 infection at Hospital HC-UNICAMP from March/20 to March/21.

Results
Of the 650 patients included in the study, 139 (21.38%) died. Comparing the patients who died vs those who survived, we observed a statistically significant difference in the occurrence of thromboembolic and vascular events (23% vs 9.8%; OR 1.332; 95%CI 1.12-1.59; p &lt; 0,0001), ICU admission (84.9% vs 39.6%; OR 0.675; 95%CI 0.62-0.74; p&lt; 0.0001) and the occurrence of HI: bloodstream infections (30.2% vs 8.6%; OR 1.62; 95%CI 1.31-1.99; p&lt; 0.0001), VAP (52.5% vs 12.3%; OR 1.882; 95%CI 1.57-2.26; p&lt; 0.0001) and UTI (27.3% vs 7.2%; OR 1.672; 95%CI 1.32-2.11; p&lt; 0.0001). Gram negative bacteria were the most isolated (62.1%), especially K. pneumoniae, A. baumannii and P. aeruginosa, followed by gram positive bacteria (27%) and fungi (13.8%).
When evaluating patients who had thromboembolic events, we observed a statistically significant association with male gender (15.9% vs 7.9%; p 0.003), mean initial D-Dimer values (10,418.00 ng/mL vs 3011.34 ng/ml; p 0.003); acute renal failure (19.1% vs 9.3%; p 0.001) and the occurrence of HI (24.4% vs 7.3%; p&lt; 0.0001).
The following factors associated with ICU admission were identified: diabetes mellitus (59.3% vs 40.5%; p&lt; 0.0001); obesity (58.3% vs 41.7%; p 0.003); O2 saturation at admission &lt; 88% (67.8% vs 32.2%); acute renal failure (78.6% vs 21.4%; p&lt; 0.0001) and the occurrence of HI (87.8% vs 12.2%; p&lt; 0.0001).
Logistic regression analysis identified the following variables independently associated with death: age (OR 1,034; CI 1,015-1,052), ICU admission (OR 1,107; CI 1,596-5,868), use of vasoactive drugs (OR 2,93; CI 1,79-4,82), development of acute renal failure (OR 7,756; CI 4,537-13,26), and the occurrence of VAP (OR 2,205; CI 1,227-3,961) (Table 1). Table 1:Variables associated to death in Logistic Regression

Conclusion
Adverse events, particularly HI, have an important impact on the evolution of patients with COVID-19, reinforcing the need for prevention and control measures to be optimized as an essential part of the care for these patients.

Disclosures
Maitê V. Luz, n/a, FAPESP: Grant/Research Support Julian F. Silva, MD, FAPESP: Grant/Research Support Hugo D. Ceccato, MD, FAPESP: Grant/Research Support Mariângela R. Resende, PhD, FAPESP: Grant/Research Support Mônica C. Pereira, PhD, FAPESP: Grant/Research Support Lucieni O. Conterno, PhD, FAPESP: Grant/Research Support.
285. Post-COVID-19 Functional Status (PCFS) scale in Mexican adults: a cross-sectional study
Authors: Hernandez Lucia Martinez , Vargas-Vazquez Tania , Guerrero-Torres Lorena Lorena 
Published: December 2022

Abstract

Background
Over 5.74 million COVID-19 cases have been reported in Mexico as of May 1, 2022. Determining the impact of COVID-19 on functional status is essential to assess health services needs. The Post-COVID-19 Functional Status Scale (PCFS) is a patient-reported tool that evaluates functional status over time after COVID-19, listing a wide range of functional limitations. We aimed to assess the functional status of Mexican patients after recovery from COVID-19. Figure 1.Persistent Symptoms acording the PCFS scale.

Methods
This cross-sectional study was conducted from April 11 to May 1, 2022, through an online survey that included demographic and clinical data, PCFS grades 0-4 and persistent symptoms. We included Mexicans aged ≥18 years who recovered from COVID-19 (≥14 days since diagnosis), who resided in Mexico and agreed to participate. We posted the survey on Facebook and Twitter. We performed a descriptive analysis of demographic and clinical variables and assessed the relationship between symptoms and PCFS grade. Statistical analyses were conducted in Stata/SE 17.0.

Results
Of 959 respondents, 838 (87%) met inclusion and exclusion criteria. Mean age was 40 (IQR 34-46) years, 82% were female, and 40% lived in Mexico City. COVID-19 diagnosis ranged from March 21, 2020, to April 7, 2022, and mean days since diagnosis was 276 (IQR 91-480) days. Most (796, 95%) were treated as outpatients. In PCFS, 338 (40%) had no functional limitations (grade 0), 266 (32%) had negligible functional limitations (grade 1), 154 (18%) had slight functional limitations (grade 2), 44 (5%) had moderate functional limitations (grade 3), 12 (2%) had severe functional limitations (grade 4) and 24 (3%) had missing PCFS data. Overall, 654 (78%) completed the persistent symptoms section. Among them, 57% presented fatigue, 46% impaired concentration, and 10% were asymptomatic (Figure 1). Of those with &gt;12 weeks since diagnosis, 88% (499/564) had at least one symptom.

Conclusion
Although most participants had mild COVID-19 at diagnosis, we found a high prevalence of persistent symptoms (90%) and functional limitations (60%) after recovery, revealing the devastating impact of COVID-19 on quality of life. The PCFS may be a valuable and simple tool to screen patients who could benefit from referral to rehabilitation programs, particularly in resource-limited settings.

Disclosures
All Authors: No reported disclosures.
292. Risk factor and clinical characteristics of pneumothorax and pneumomediastinum in COVID-19: a matched case-control study
Authors: Lee Se Ju , Kim Jinnam , Lee Ki Hyun , Lee Jung Ah , Kim Chang Hyup , Lee Su Hwan , Yeom Joon-sup , Ku Nam Su , Jeong Su Jin , Ahn Jin Young , Kim Jung Ho , Choi Jun Yong 
Published: December 2022

Abstract

Background
During the novel coronavirus SARS-CoV-2 pandemic, a considerable number of pneumothorax and pneumomediastinum associated with COVID-19 have been reported, and the incidence was higher in critically ill patients. Despite using a protective ventilation strategy, barotrauma still occurs in COVID-19 patients with invasive mechanical ventilation. This study aims to identify the risk factors and clinical characteristics of pneumothorax and pneumomediastinum in COVID-19 by a matched case-control study.

Methods
This retrospective study enrolled adult patients diagnosed with a COVID-19, admitted to a critical care unit in South Korea from 2020 March 1st to 2022 January 31st. COVID-19 patients with pneumothorax and pneumomediastinum were compared, in a 1 to 2 ratio, to a control group of COVID-19 patients without pneumothorax and pneumomediastinum, matched on age, gender, and worst National Institute of Allergy and Infectious Diseases ordinal scale (NIAID-OS). Conditional logistic regression analysis was performed to assess the risk factors for pneumothorax and pneumomediastinum in COVID-19.

Results
A total of 427 patients with COVID-19 were admitted during the study period. Of these patients, 24 patients were diagnosed as pneumothorax or pneumomediastinum. When comparing the characteristics of both groups, body mass index (BMI) was significantly lower in the case group (22.8 kg/m2 and 24.7 kg/m2; P = 0.048). BMI was statistically significant risk factor for barotrauma in univariate conditional logistic regression analysis (Odds ratio (OR), 0.85; Confidence interval (CI), 0.72-0.996; P = 0.044) but not in multivariate analysis. For the patients with invasive mechanical ventilation, the period from symptom onset to intubation was longer in the case-patients (13 and 9.5 days; P = 0.032). Univariate conditional logistic regression analysis showed the statistical significance of the period from symptom onset to intubation (OR, 1.14; CI, 1.006-1.293; P = 0.041).

Conclusion
In this case-control study with age, gender, severity matching, lower BMI was associated with the pneumothorax in COVID-19, and delayed application of invasive mechanical ventilation might contribute to this complication.

Disclosures
All Authors: No reported disclosures.
298. Successful Treatment of Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Infection in an Immunocompromised Patient
Authors: Overbeck Victoria , Turcinovic Jacquelyn , Qiu Xueting , Seitz Scott , Connor John , Schaeffer Beau , Hanage William P , Curry Scott R , Kuppalli Krutika 
Published: December 2022

Abstract

Background
The COVID-19 pandemic has been marked by long-term persistence of SARS-CoV-2 in immunocompromised patients receiving B-cell-depleting therapies, with many individuals experiencing fatal COVID-19.

Methods
We report an individual treated with rituximab who survived persistent COVID-19 over 9 months. SARS-CoV-2 positive RNA samples were sequenced using targeted amplicon NGS sequencing with backup sequencing on a nanopore platform. The resulting sequences were analyzed for genomic variance over time at the consensus and sub-consensus level.

Results
An individual with rheumatoid arthritis (RA) treated with azathioprine and rituximab (last dose in May 2020) was diagnosed with COVID-19 in July 2020 and admitted with pneumonia. After initial incomplete recovery, the patient had persistent infection through March 2021 and received both remdesivir and convalescent plasma (January 2021). The patient received three doses of mRNA vaccine (Pfizer BioNTech) in December 2020, April 2021, and November 2021, but was seronegative for nucleocapsid IgG in both January 2021 and March 2021; positive spike IgG developed by September 2021 (512 AU/ml) and December 2021 (621 AU/ml) (Figure 1). The patient recovered with new oxygen dependence (2-3L) and manages RA off B-cell depletion; they required an extended corticosteroid taper to manage organizing pneumonia and treatment for several opportunistic infections.
Viral sequencing over the course of illness indicated a persistent infection with a lineage B.1.585.3 virus that accumulated 14 mutations throughout the infection. Two mutations (S494P, S D737Y) are associated with therapy resistance and are similar to those found in other immunocompromised individuals with persistent COVID-19. Additional mutations were of unknown consequence. Figure 1:Timeline of Immunocompromised Patient’s Clinical Course of COVID-19

Conclusion
SARS-CoV-2 was able to establish persistent infection and accumulated mutations associated with therapeutic resistance; repeated vaccination was associated with successful resolution following repeated vaccination after stopping rituximab. Cessation of B-cell-depleting therapy was likely the critical factor in the patient’s recovery, but repeated vaccination was associated with a delayed seroconversion in this patient with reversibly immunosuppression.

Disclosures
William P. Hanage, PhD, Biobot Analytics Inc: Advisor/Consultant|Merck Vaccines: Advisor/Consultant.
326. Optimizing DNA Extraction from Pediatric Stool for Diagnosing Tuberculosis and Use in Next Generation Sequencing
Authors: Ness Tara , Meiwes Lennard A , Kay Alexander , Mejia Rojelio , Lange Christoph , Mandalakas Anna , DiNardo Andrew 
Published: December 2022

Abstract

Background
Next generation sequencing (NGS) is quickly coming to the forefront of diagnostic tools to provide efficient, highly informative information from patient samples. Recently, it was established that patients with pulmonary Tuberculosis (TB) have Mycobacterium tuberculosis DNA present in their stool samples, which can augment current diagnostic gaps. Optimizing extraction of DNA from stool for analysis via sequencing technologies is a paramount initial step to ensure accuracy of downstream sequencing applications.

Methods
Attenuated strains of Mycobacterium bovis derived from BCG were used as a model for Mtb. Human stool samples were spiked with varying known concentrations of BCG and extracted with four different DNA extraction kits (Fast DNA Spik Kit for Soil, DNeasy Blood and Tissue Kit, MagAttract HMW DNA Kit, and PowerFecal Pro DNA Kit). Each sample was subjected to quantitative polymerase chain reaction using designed primers and probes specific for identifying Mtb infection from stool. The samples underwent further analysis to assess overall DNA yield (Qubit fluorometer), DNA fragment length (Agilent tape measure), and DNA purity (Nanodrop spectrophotometer).

Results
Overall, the Fast DNA Spin Kit for Soil extraction kit showed the most optimal results. DNA isolated via this method showed the lowest cycle thresholds of Mtb amplification, indicating the most preserved amount of BCG specific DNA. In addition, this method showed the highest overall DNA yield and highest proportion of long DNA fragment lengths. Fluorometric analysis showed significant contamination in the 230 nm wavelength range, which was amended with an additional AMPure bead cleanup step.
Quantiative PCR of Spiked BCG
Quantitative PCR Cycle Threshold Values by Different DNA Extraction Kits

Conclusion
The MPFast Soil Extraction kit, when compared to three other DNA extraction kits, performed the best on stool samples for isolating BCG DNA. Overall DNA yield, DNA length, and amount of specific BCG DNA were best optimized with this method and provided the best samples for sequencing analysis. This critical step is the first of many to realize the promise of stool-based NGS.
DNA Quantity
Quantity of Total DNA by Different DNA Extraction Kits
Spectrophotometric Analysis
Analysis of Absorption of Extracted DNA by Different DNA Extraction Kits
Spectrophotometric Results
Spectrophotometry Results of DNA Samples Extracted by Different DNA Extraction Kits

Disclosures
Lennard A. Meiwes, n/a, German Center for Infection Research (DZIF): Grant/Research Support.
328. Universal PCR Testing- Is It Worth It?
Authors: Birk Navina K , Saikia Kasturi , Ramesh Mayur , Samuel Linoj , Tibbetts Robert 
Published: December 2022

Abstract

Background
Universal PCR and Next Generation Sequencing (uPCR/NGS) is a major advancement in microbiology. It is a highly sensitive and specific test that amplifies ribosomal RNA in samples to detect bacterial and fungal pathogens. We investigated the uPCR/NGS tests sent from Henry Ford Health (HFH) and the effect obtaining this test had on patient care.

Methods
We completed a retrospective, observational study assessing all consecutive uPCR/NGS tests obtained from at HFH from 2016-2021. This included uPCR/NGS for detection of bacterial, fungal, mycobacterium tuberculosis (MTB), and non-tuberculosis mycobacterium (NTM). All samples were of non-blood fluids and tissue samples. Patients concurrent tissue cultures and blood cultures from day of uPCR/NGS, and within 6 months of obtaining the uPCR/NGS sample were evaluated. Primary outcomes included if uPCR/NGS testing resulted in a change of choice or duration of antibiotic therapy.

Results
At HFH, 226 uPCR/NGS tests from 111 samples were analyzed. This included 83 bacterial, 51 MTB, 51 NTM, and 41 fungal uPCR/NGS tests. Of the 226 uPCR/NGS tests, 31 tests (13.7%) resulted with positive result on uPCR/NGS. A total of 31 tests (13.7%) were ordered on a known culture positive sample, and 195 (86.3%) were ordered on a culture negative sample.
Of samples sent from a culture positive sample, 7 (22.6%) resulted with positive uPCR/NGS results. 3 (42.9%) matched the tissue cultures, and 2 (28.6%) matched the patients’ blood cultures. None of the patients had any change in choice or duration of antibiotics based on uPCR/NGS results.
Of the samples sent from a culture negative sample, 24 (12.3%) samples resulted with positive uPCR/NGS results. 2 (8.3%) matched a patient’s tissue cultures and none matched blood cultures. Change in antibiotic choice or duration occurred in 16 (17.6%) patients. The samples with the highest rates of change in management included cerebrospinal fluid (42.9%), brain tissue (36.4%), cardiac valvular tissue (27.3%), lymph nodes (25%), synovial fluid (20%). Figure 1:Flowchart of Results and Impact on Management

Conclusion
Our results show that uPCR/NGS has an overall low percent of impact in clinical outcomes, but it is a useful test in when used on a culture negative sample in certain sample types, along with a high index of suspicion for infection.

Disclosures
All Authors: No reported disclosures.