bluuebunny/crossref_metadata_2025_split huggingface dataset:
1331. Seasonality of Common Human Coronaviruses in the United States, 2014-2021
Authors: Shah Melisa , Haynes Amber K , Dahl Rebecca M , Kniss Krista , Silk Benjamin , Killerby Marie E 
Published: December 2021

Abstract

Background
The four common human coronavirus (HCoV) types, including two alpha (NL63 and 229E) and two beta (HKU1 and OC43) coronaviruses, generally cause mild, upper respiratory illness. Common HCoV seroprevalence increases rapidly during the first five years of life and remains high throughout adulthood. HCoVs are known to have seasonal patterns, with variation in predominant types each year, but more defined measures of seasonality are needed.

Methods
We describe laboratory detection, percent positivity, and seasonality of the four common HCoVs during July 2014 to May 2021 in the United States reported to the National Respiratory and Enteric Virus Surveillance System (NREVSS). We also describe age, sex, and co-detection with other respiratory viruses for a subset of specimens available through the Public Health Laboratory Interoperability Project (PHLIP). We used a method previously validated for respiratory syncytial virus, characterized by a centered 5-week moving average and normalization to peak, to define seasonal inflections, including season onset, peak, and offset.

Results
Any HCoV type was detected in 96,336 (3.4%) of 2,487,736 specimens. Predominant common HCoV types fluctuated by surveillance year (Figure 1) and were generally consistent across geographic regions. In a subset of 4,576 specimens with a common HCoV detection, those with type 229E had a higher median age compared to other HCoV types (30.8 versus 24.8 years, p&lt; 0.001), but there were no differences by sex. Influenza was the most commonly co-detected virus. In the last six complete HCoV seasons, onsets ranged from October to November, peaks from January to February, and offsets from April to June; &gt;95% of all HCoV detections occurred within these ranges. The 2020-2021 common HCoV season onset, dominated by types NL63 and OC43, was delayed by approximately two months compared to prior seasons.

Figure 1. The top panel represents total specimens tested and the bottom panel shows percent positivity of the four common human coronavirus (HCoV) types by week starting July 5, 2014 through May 8, 2021. Data are from the National Respiratory and Enteric Virus Surveillance System (NREVSS).

Conclusion
Common HCoVs demonstrate relatively consistent seasonal patterns. The delayed onset of the 2020-2021 season may be attributable to mitigation measures implemented across the US including masking, improved hand hygiene, and social distancing. Better defining HCoV seasonality can inform clinical preparedness and testing practices and may provide insights into the behavior of emerging coronaviruses.

Disclosures
All Authors: No reported disclosures
1339. Impact of COVID-19 Pandemic on Activity of Other Respiratory Viral Pathogen and Norovirus
Authors: DiBiase Lauren , Sickbert-Bennett Emily , Weber David J , Weber David J , Miller Melissa B 
Published: December 2021

Abstract

Background
The COVID-19 pandemic led to the implementation of several strategies (e.g., masking, physical distancing, daycare/school and business closures, hand hygiene, surface disinfection) intended to mitigate the spread of disease in the community. Our objective was to evaluate the impact of these strategies on the activity of respiratory viral pathogens (other than SARS-CoV-2) and norovirus.

Methods
At University of North Carolina (UNC) Hospitals, we compared the percent positivity for respiratory viral pathogens and norovirus by calendar year for 2014-2019 and the first three months of 2020 to the percent positivity in the subsequent months of 2020 and the first quarter of 2021. Patients were included in the study if they had a positive specimen obtained in a clinic, ED or as an inpatient. Three molecular tests were used to detect these viruses: adenoviruses, endemic coronaviruses (OC43, 229E, NL63, HKU1), influenza A (subtypes H3, H1, H1N1pdm), influenza B, metapneumovirus (MPV), parainfluenza viruses 1-4 (PIV), rhinovirus and/or enterovirus (RhV/EV), and respiratory syncytial virus (RSV). Two molecular tests were used to detect norovirus. We calculated point prevalence rates with 95% confidence intervals to assess statistical differences in percent positivity.

Results
There was a statistically significant decline in percent positivity for endemic coronaviruses, influenza, MPV, PIV, RSV and norovirus during the time-periods after March 2020 when compared to all other time-periods (Figure). RhV/EV, followed by adenovirus were the most prevalent types of respiratory viruses circulating during height of COVID-19. There was a statistically significant decline seen in RhV/EV in April-Dec 2020, but activity increased in 2021. There was no difference seen in adenovirus activity across time-periods.
Percent Positivity of Respiratory Viral Pathogens and Norovirus by Time Period

Conclusion
Our study demonstrated statistically significant decreases in the percent positivity of several respiratory viral pathogens, as well as norovirus, during the time-period of high community prevalence of SARS-CoV-2. Strategies put in place to mitigate SARS-CoV-2 transmission likely contributed to these differences. Non-enveloped viruses like rhinovirus and adenoviruses may have been less impacted by these strategies since they are more resistant to disinfection.

Disclosures
David J. Weber, MD, MPH, PDI (Consultant) Melissa B. Miller, PhD, D(ABMM), F(AAM), Abbott Molecular (Grant/Research Support)Agena Bioscience (Consultant)ArcBio (Grant/Research Support)Cepheid (Consultant)Luminex Molecular Diagnostics (Consultant)QIAGEN (Consultant)Sherlock Biosciences (Consultant)Talis Biomedical (Consultant)Werfen (Consultant)
1347. Comparison Between SARS-Cov-2, non-SARS-Cov-2 Coronavirus, Influenza and RSV Infections Among Solid Organ Transplant Recipients
Authors: Mendoza Maria A , Gabriel Motoa , Raja Mohammed , Anjan Shweta , Fernandez Anmary A , Courel Steve , Chandorkar Aditya , O’Brien Christopher , Phancao Anita , Sinha Neeraj , Vianna Rodrigo , Gaetano Ciancio , Loebe Mathias , Simkins Jacques , Camargo Jose F , Morris Michele I , Abbo Lilian M , Guerra Giselle , Natori Yoichiro 
Published: December 2021

Abstract

Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been raging since the end of 2019 and has shown worse outcomes in solid organ transplant recipients (SOTR). The clinical differences as well as outcomes between these respiratory viruses have not been well defined in SOTR.

Methods
This is a retrospective cohort study of adult SOTR with nasopharyngeal swab or bronchoalveolar lavage PCR positive for either SARS-CoV-2, non-SARS-CoV-2 coronavirus, influenza, or respiratory syncytial virus (RSV) from January 2017 to October 2020; both inpatient and outpatient. The follow up period was up to three months. Clinical characteristics and outcomes were evaluated. Development of lower respiratory tract infection (LRTI) was defined as new pulmonary infiltrates with or without symptoms. For statistical analysis, Fischer’s exact test and log rank test were performed.

Results
During study period, 157 SARS-CoV-2, 72 non-SARS-CoV-2 coronavirus, 100 influenza, 50 RSV infections were identified. Patient characteristics and outcomes are shown in tables 1 and 2, respectively. Secondary infections were not statistically significantly different between SARS-CoV-2 vs. non-SARS-CoV-2 coronavirus and influenza (p=0.25, 0.56) respectively, while it was statistically significant between SARS-CoV-2 and RSV (p=0.0009). Development of LRTI was higher in SARS-CoV-2 when compared to non-SARS-CoV-2 coronavirus (p=0.03), influenza (p=0.0001) and RSV (p=0.003). Admission to ICU was higher with SARS-CoV-2 compared to non-SARS-CoV-2 coronavirus (p=0.01), influenza (p=0.0001) and RSV (p=0.007). SARS-CoV-2 also had higher rates of mechanical ventilation when compared to non-SARS-CoV-2 coronavirus (p=0.01), influenza (p=0.01) and RSV (p=0.03). With time to event analysis, higher mortality with SARS-CoV-2 as compared to non-SARS-CoV-2 coronavirus, influenza, and RSV (p=0.01) was shown (Figure 1).

Figure 1. Kaplan Meier Curve: Comparison of Mortality between SARS-CoV-2, non-SARS-CoV-2 coronavirus, influenza and RSV

Conclusion
We found higher incidence of ICU admission, mechanical ventilation, and mortality among SARS-CoV-2 SOTR vs other respiratory viruses. To validate these results, multicenter study is warranted.

Disclosures
All Authors: No reported disclosures
1350. Characterization of the Type of Specimen Used for Testing of Sexually Transmitted Infections in Outpatient Clinics
Authors: Sittig Katherine , Cunningham Victoria C , Rosa Rossana , Veach Lisa A 
Published: December 2021

Abstract

Background
Screening and diagnosis of Sexually Transmitted Infections (STIs) requires use of nucleic acid amplifications tests (NAATs) on optimal anatomical specimens. Vaginal or cervical swabs are preferred in women and first-catch urine in men. Furthermore, extra-genital testing is recommended for men who have sex with men (MSM) and for men who have sex with women (MSW) based on exposure history. Increasingly, STI care is being provided in non-STI specialized settings such as Urgent Care (UC) and Primary Care clinics (PC). Therefore, we aimed to characterize the types of anatomical specimens being utilized for the diagnosis of STIs in non-STI specialized clinics.

Methods
We conducted a retrospective analysis of all Neisseria gonorrhea (GC) and Chlamydia trachomatis (CT) tests obtained at 46 adult outpatient clinics (PC, UC and Obstetrics & Gynecology [OB/Gyn]) part of an integrated health system in Des Moines, Iowa, between January 1, 2019 and December 31, 2019. In this database, no information was available regarding patient history of sexual exposure site(s). Descriptive statistics, including counts, percentages, and differences in proportions were estimated and stratified by outpatient clinic type.

Results
We identified a total of 18,503 encounters involving 2,802 men and 15,701 women. Rates of extragenital testing were overall low, but higher in male patients (14.6%) than in female patients (0.20%). Among male patients, extra-genital testing was obtained in 21.1% of patients seen in PCs compared to 5.2% in UCs (p&lt; 0.0001) (Table 1). Notably, 177 (50.9%) of the extra-genital samples collected at PCs were obtained at a clinic specializing in the care of MSM. Among female patients, the proportion of urine-based tests was highest in PC (32%), while non-urine genitourinary samples were more frequently obtained at Ob-Gyn clinics (92.7%) (p&lt; 0.0001) (Table 2).

Conclusion
Extragenital site testing for GC and CT remains an uncommon practice across all clinic setting types, and high proportions of female patients evaluated at PC and UC clinics were tested using urine specimens. Our results indicate a need for effective education and implementation processes for optimal testing modalities in primary care clinics.

Disclosures
All Authors: No reported disclosures
1354. Antibiotic Resistance and Coinfections Among Women with Sexually Transmitted Infections
Authors: Carpenter Brittany L , Peacock Jacqueline D , Dubiak Kyle , Fecteau Heather , Carlson Robert 
Published: December 2021

Abstract

Background
Sexually transmitted infections (STIs) represent a growing epidemic, particularly among America’s youth. Traditional single or dual organism STI testing is limited in its utility compared to PCR panel-based vaginitis testing. PCR panel testing can identify up to 99% of vaginitis associated organisms, while simultaneously providing information about antibiotic resistance.

Methods
We analyzed 10,011 vaginosis panel cases released between April 2020 and May 2021. The PCR-based vaginosis panel consists of organisms associated with bacterial vaginosis, aerobic vaginitis, yeast infections, STIs, and Lactobacillus species. This panel simultaneously detects evidence of antibiotic resistance for nine classes of drugs.

Results
Of 9405 cases from vaginal swabs, 618 (6.8%) were positive for at least one STI including Chlamydia trachomatis (CT), Haemophilus ducreyi, Herpes Simplex Virus 1 or 2 (HSV2), Neisseria gonorrhoeae (NG), and/or Trichomonas vaginalis. Of 603 urine samples, 7.6% were positive for at least one STI and represented a younger population. Patients younger than age 25 (33% of the cohort) were disproportionately affected by STIs, consistent with CDC findings. About 50% of all positive STI cases were in patients under 25. Evidence of bacterial vaginosis was also present in 89% of CT and NG cases, and 75% of HSV2 cases. Strikingly, we found the presence of an antibiotic resistant marker(s) to first line treatment in 76.2% of CT and 19.3% of NG cases.

Conclusion
Our data illustrates the advantages of utilizing a PCR-panel approach to STI detection over a targeted approach for individual organisms. Coinfections with bacterial vaginosis were common and if left unidentified, patients may receive incomplete treatment. Additionally, our data suggests that antibiotic resistance testing is imperative for effective treatment planning and antibiotic stewardship in suspected STI cases.

Disclosures
Brittany L. Carpenter, PhD, NxGen MDx (Employee) Jacqueline D. Peacock, PhD, MB(ASCP)CM, NxGen MDx (Employee) Kyle Dubiak, PhD, NxGen MDx (Employee) Heather Fecteau, MS, LCGC, NxGen MDx (Employee) Robert Carlson, MD, FCAP, NxGen MDx (Employee)
1367. Management of Patients Presenting with Purulent Skin and Soft Tissue Infections in the Emergency Department (ED)
Authors: Son Andrea , Hecker Michelle 
Published: December 2021

Abstract

Background
Incision and drainage (I&D) is the primary treatment for purulent skin and soft tissue infection (SSTI). Empiric adjunctive treatment of purulent SSTI targets methicillin-resistant Staphylococcus aureus (MRSA). In light of increasing antibiotic resistance, culture and sensitivity (C&S) from drained specimen and consideration of the local antibiogram are recommended.1 Our primary objective was to assess the utilization of C&S from drained specimen in out institution’s ED. Our secondary objectives were to describe antibiotic choice and duration of therapy upon discharge, to evaluate the appropriateness of antibiotic choice based on C&S and local antibiogram, and to assess the need for adjunctive antibiotic based on available literatures.

Methods
A retrospective cohort study was performed on a random sample of unique patients who underwent I&D procedure in the ED from January 2019 through December 2019. Demographic and clinical data were collected from the electronic medical record.

Results
Of 120 patients evaluated, only 14 patients (11.7%) had C&S performed on the initial I&D specimen (Table 1). Five patients received inappropriate antibiotic(s) based on C&S. Of 108 patients who were discharged from ED, antibiotic(s) was prescribed in 97 patients (Table 2). Mean duration of therapy was 7.8 days with 27.8% of patients prescribed a duration of therapy longer than 7 days. Despite high clindamycin resistant rate for MRSA (35%), clindamycin was the second most prescribed antibiotic. Adjunctive antibiotic(s) may have been unnecessary in 9.5% patients. Five patients reported possible adverse reaction related to prescribed antibiotic. Additional antibiotic course was prescribed in 15 patients for the same infection. Fifteen patients were readmitted to ED within 30 days and five of them required hospital admission

Conclusion
At our institution, majority of patients were discharged after I&D with adjunctive antibiotic(s) without microbiologic testing. Despite high local clindamycin resistance, it was the second most commonly prescribed empiric treatment. Developing a clinical pathway that emphasizes the importance of timely microbiologic testing and local antibiogram consideration along with the need for appropriate adjunctive antibiotics may improve patient outcomes.

Disclosures
All Authors: No reported disclosures
1374. Clinical Outcomes of Sepsis According to Race at University of Minnesota Medical Center
Authors: Meyer-Mueller Cameron , Williams Darlisha A , Westerhaus Michael , Rajasingham Radha 
Published: December 2021

Abstract

Background
Sepsis is a life-threatening condition associated with significant in-hospital mortality. Sepsis disproportionately affects Black Americans and is a top-10 leading cause of death for Black people. Previous studies examining sepsis mortality rates by race have yielded inconsistent findings. This retrospective study evaluates the relationship between race and in-hospital sepsis-related mortality in adults at University of Minnesota Medical Center.

Methods
We reviewed all sepsis diagnoses in adults between January 1, 2020 and June 30, 2020 at the University of Minnesota Medical Center. Demographic information including age, sex, race, insurance status, primary language, expected and observed mortality score, discharge status, treatment information, and in-hospital mortality were also recorded. Self-reported race was categorized as African American, White, American Indian or Alaska Native, Asian, African, Hispanic or Latino, Hawaiian or other Pacific Islander, “some other race,” and “two or more races.” Statistical tests including χ  2 test, Student t test, Kaplan-Meier estimator, and binary logistic regression were performed.

Results
We identified 780 cases of sepsis. Black patients were consistently younger than White patients (median age of 50 years, compared to 61 years, p&lt; 0.001). Black patients were more likely to have comorbidities at baseline. However, logistic regression analyses, after controlling for language, race, primary payer, and expected mortality, showed no association between sepsis outcome and race.
Sepsis Cases at UMMC between January and June 2020 by Self-Reported Race

*Other includes the categories “Some other race” and “Two or more races.”
Hospital Outcomes by Race

Patient Demographics by Race

Conclusion
While there was no significant difference between in-hospital mortality and race, Black patients were more likely to present at a younger age with more medical comorbidities than White patients.

Disclosures
All Authors: No reported disclosures
157. Impact of Pharmacist-Generated Oral Antimicrobial Test Prescription on Discharge Medication Access and Outcome
Authors: Mulugeta Surafel , Davis Susan L , Davis Susan L , Kenney Rachel 
Published: December 2021

Abstract

Background
Cost barriers to accessing discharge oral antimicrobials (ABX) may delay discharges and result in suboptimal discharge ABX. Use of electronic test prescriptions (eTP) or “price checks” is controversial due to potential for erroneous dispensing. This study evaluated discharge ABX access and outcome after implementation of a standardized, inpatient pharmacist-initiated ABX eTP process in collaboration with discharge pharmacy.

Methods
IRB approved, retrospective, cross-sectional cohort pilot-study. Inclusion: home bound adults admitted for ≥ 72 hours from 1/1/18-2/28/19 and discharged on oral ABX. Patients with an ABX eTP prior to discharge were compared to those discharged on ABX but no eTP. Data were reported using descriptive statistics and bivariate analysis. Primary endpoint: discharge delay after medical stability. Secondary endpoints: medication access, unplanned encounters, and % of patients discharged on first-line ABX.

Results
84 patients included: 43 no-ETP and 41 eTP. 75 ABX eTP evaluated among 41 patients. Patients in the no-eTP group had higher Charlson comorbidity index (P = 0.004) and immunosuppression (24% vs. 12%; P = 0.014). Median length of stay, days: 6 (5 – 9) eTP vs. 8 (5 – 15) no-eTP (P = 0.026). Most common eTP requested by pharmacist: linezolid (17, 23%) and oral vancomycin (12, 16%) (Figure 1). eTP results were documented in the medical record in &lt; 24 hours for 66 (88%) of inquiries. 49 (65%) prescriptions were approved by insurance; 16 (21%) had no out of pocket cost and 8 (11%) required prior authorization (PA) (Table 1). Linezolid (5, 35%) and public insurance (10, 71%) were frequently associated with barriers. 29 (70%) patients were discharged on the same ABX as the eTP. There were no discharge delays or erroneous dispensing. 14 (33%) no-eTP and 15 (37%) eTP patients experienced unplanned healthcare encounters after discharge. 9/84 (11%) patients were discharged on suboptimal ABX. Non-white race 8/9 (89%) P = 0.047 and public insurance 8/9 (89%) P = 0.063 were associated with suboptimal discharge ABX.
Figure 1. Oral Antimicrobial Test Prescription Pattern (n=75)

Table 1. Oral Antimicrobial Test Prescription Result (n=75)

Conclusion
A standardized eTP process appears to be a safe way to evaluate out of pocket cost without prolonging length of stay. Future work will focus on inequity in access to first line ABX.

Disclosures
Susan L. Davis, PharmD, Nothing to disclose Rachel Kenney, PharmD, Medtronic, Inc. (Other Financial or Material Support, spouse is an employee and shareholder)
1381. Do Gut Microbiome Profiles Correlate with Hospital Length of Stay During Hematopoietic Stem Cell Transplantation?
Authors: Mendy Angelico , Tierney Kitty , Mink Tara , Hussein Walaa , Monaco Peter , Weinstein Claire , Kandala Prathyusha , Wilkinson Racheal , Patel Kavya , Apewokin Senu 
Published: December 2021

Abstract

Background
Length of stay is not only an indicator of how successful a hospitalized patient’s treatment and recovery is, but is also an indicator of fiscal costs to the hospital. Hematopoietic stem cell transplants (HSCT) patients typically experience extended hospital admissions that can vary significantly patient to patient with hospital discharge dependent upon a recovered white blood cell count. Recent literature suggests a gut microbial influence on hematopoiesis. We sought to explore potential associations between gut microbiome diversity and the length of stay in patients undergoing HSCT in the inpatient setting.

Methods
Within two healthcare systems, we identified patients who would receive conditioning chemotherapy and subsequent HSCT in the inpatient setting. Pre-chemotherapy stool was collected, sequenced with shotgun metagenomics, and analyzed for gut microbial diversity using Inverse-Simpson index. The length of admission or length of stay during their transplant process was recorded. We assessed whether there was an association with gut microbial diversity and length of stay.

Results
24 patients we evaluated for diversity and length of stay. There was no significant correlation between age or gender and length of stay. Significant difference in length of stay was seen between allogenic vs autogenic transplants (p value ≤0.01). Within the 24 patients, lengths of stay ranged from 8 to 36 days with a mean average of 20.9 days. Gut diversity ranged from 1.8 to 23.9. An overall negative association between length of stay and diversity was seen, though this was determined not statistically significant (p value 0.09).
Length of Stay correlation with pre-chemotherapy Gut Microbiome diversity

Conclusion
Our study showed no significant association between gut microbial diversity and inpatient length of stay during HSCT. Overall, a trend towards increased length of stay in patients with decreased diversity was noted. Additional studies of greater participant size are necessary to confirm or further study these findings.

Disclosures
All Authors: No reported disclosures