bluuebunny/crossref_metadata_2025_split huggingface dataset:
825. An Academic-Information Technology Partnership to Create an Infectious Diseases Translational Science Database
Authors: Lancaster Christopher K , Gonzales-Luna Anne J , Beairsto Jeffrey , Neptune Randal , Killen Joanna , Dugas Corey , Webster Beth , Rutter John N , Rutter Tristan , Garey Kevin W 
Published: January 2021

Abstract

Background
Translational science is the process of turning observations in the laboratory, clinic, and community into interventions that improve human health. The coordinated effort to maintain integrated, validated laboratory and clinical data is often a rate-limiting step for research laboratories, especially for multi-site studies. Previous research shows a rate of error between 2.3 and 5.2% for basic data collection in clinical databases, up to 26.9% for more complex data points. The purpose of this project was to create a translational science database prototype that would be responsive to the unmet needs of the translational research community.

Methods
Translational scientists, IT experts, and lab technicians mapped the workflow of a high-throughput research laboratory including clinical and laboratory data. Database goals were to develop processes that would minimize data entry time, avoid redundancies, and validate data in a secure environment (HIPAA-compliant). Unique to this platform was the ability to map creation of new samples (for example, PCR products) from parent samples (biologic samples). The platform was developed in an iterative process utilizing interviews, workflow study, analysis of supporting artifacts, and mock-ups.

Results
The current prototype allows for electronic upload or manual data entry of clinical data. In a small controlled study we found the rate of error for basic data entry to be below 1% within it. Pre-populated data entry screens map laboratory work-flow with custom data entry fields produced based on laboratory results earlier in the work flow. Work-flow mapping includes microbiology, phenotypic descriptions (MIC), molecular biology (PCR), and customized experiments. Sequence data, housed separately, has data linkers stored in the database. The launch screen and data entry forms are populated based on specific criteria entered for each user.

Conclusion
The Translational Science Database allows for efficient capture of high-quality data with baseline validation enabling seamless linking of translational data for single or multi-site laboratories. Future development work will expand the number of experiments and also incorporate stored biobank information into the database.

Disclosures
Jeffrey Beairsto, BSc Eng (ME), Populus (Employee, Shareholder) Randal Neptune, BSc., MSc., Populus Global Solutions (Employee) Beth Webster, BSc, MBA, Populus Global Solutions Inc (Employee, Shareholder) John N. Rutter, BscEng, Populus Global Solutions (Board Member, Employee, Shareholder) Tristan Rutter, BA, Populus (Employee) Kevin W. Garey, PharMD, MS, FASHP, Merck & Co. (Grant/Research Support, Scientific Research Study Investigator)
828. Evaluation of Home Time as a Patient-Centered Metric for Pneumonia Hospitalizations: A Retrospective Cohort Study of Medicare Fee-For-Service Beneficiaries
Authors: Nair Rajeshwari , Gao Yubo , Vaughan-Sarrazin Mary , Perencevich Eli N , Girotra Saket , Pandey Ambarish 
Published: January 2021

Abstract

Background
The Centers for Medicare & Medicaid Services (CMS) uses hospital readmission to incentivize hospital care delivery for acute conditions including pneumonia. However, current CMS performance metrics do not account for the competing risk of mortality in the post-discharge period or during the hospital stay. Our objective was to assess home time within 30 days after discharge among pneumonia hospitalizations, as a patient-centered metric.

Methods
A retrospective observational study was conducted in a cohort of Medicare fee-for-service beneficiaries admitted between 01/01/2015 and 11/30/2017. Home time was the number of days spent alive, out of an acute care setting, skilled nursing facility, or a rehabilitation facility within 30 days of discharge. If a patient spends any part of a day in a care facility or died after discharge, then that day was not included in the calculation for home time. Hospital-level rates of risk-adjusted home time were calculated using multilevel regression models. We compared hospital performance on 30-day risk-standardized home time with its performance on 30-day risk standardized readmission rate (RSRR) and mortality rate (RSMR). Characteristics of hospitals with high and low risk-adjusted home-time were compared.

Results
Among 1.7 million pneumonia admissions admitted to 3,116 hospitals, the median 30-day risk-standardized home time was 20.5 days (interquartile range: 18.9-21.9 days). Hospital-level characteristics such as case volume, bed size, for-profit ownership, rural location of hospital, teaching status, and participation in the bundle payment program were significantly associated with home-time. RSRR (rho: -0.233, p&lt; 0.0001) and RSMR (rho: -0.223, p&lt; 0.0001) had weak, inverse correlations with home time. Using the home time metric, 35.5% of hospitals were reclassified as high performers compared with their average or poor performance on the RSRR or RSMR metric.

Conclusion
Home time is a novel, patient-centered, hospital-level metric that can be easily calculated using claims data, accounts for differences in post-discharge mortality and can be intuitively interpreted. Utilization of this metric could potentially have policy implications in assessing hospital performance on delivery of healthcare to pneumonia patients.

Disclosures
Rajeshwari Nair, PhD, Merck and Company, Inc. (Research Grant or Support)
830. The effect of a long-stay patient on transmission of a pathogen to shorter-stay patients in a small multi-bed hospital unit: Implications for infection control
Authors: Ong Karen , Peskin Charles , Phillips Michael 
Published: January 2021

Abstract

Background
Objective: To quantify the effect of a long-stay patient in a hospital unit on the likelihood of colonization of that patient and other patients in the unit.
Prolonged hospital and intensive care unit (ICU) stays have been found to be risk factors for colonization and infection with bacteria such as carbapenem-resistant Enterobacteriaceae (CRE) for which there are limited treatment options and high mortality rates, making prevention of transmission and infection important public health objectives. Many studies have shown that long-stay patients (such as inpatient rehabilitation or skilled nursing facility patients) are at higher risk for hospital-acquired infections than short-stay patients, but the impact of long-stay patients on other patients in the same hospital unit has not received as much attention. Here, we consider a mathematical model of pathogen transmission within a hospital unit and assess the impact at different patient-patient transmission rates of a single long-stay patient on the probability that any other patient leaves the unit colonized with a pathogen.

Methods
We estimated the increased risk caused by a colonized long-stay patient on colonization of other patients using an ordinary differential equation Markov model with three mechanisms of colonization (pre-existing colonization, environmental transmission, and patient-patient transmission) with parameters previously estimated from a 13-bed hospital rehabilitation unit to evaluate the probability of exiting colonized.

Results
A single colonized long-stay patient increases the probability of each other patient exiting the unit colonized from 10.4% to 17.3%, a relative increase in risk of 1.4, and increases the expected number of colonized patients within the unit from 1.37 to 2.07 (not including the long-stay colonized patient).
Probability of exiting colonized from a unit with a long-stay, initially colonized patient versus the probability of exiting colonized from a unit with no long-stay patient. The solid black line indicates a unit with regular turnover, whereas the dashed black line indicates a unit with a single long-stay, initially colonized patient. The vertical line shows the value of γ = 0.002 inferred from data from a 13-bed rehabilitation unit, and the shaded regime indicates the uncertainty in this estimate (0.000329, 0.003729).

Conclusion
Colonized long-stay patients pose a risk to other uncolonized patients in the unit, especially at higher patient-patient transmission rates. Potential long-stay patients should be screened for CRE at entry and periodically during their stay because they are both at higher risk of colonization and also of transmitting bacteria to other patients. Consider increased surveillance, isolation, and/or decolonization of long-stay patients.

Disclosures
All Authors: No reported disclosures
57. Evaluating the Utility of a Penicillin Allergy Reconciliation Program within an Infectious Diseases Consult Population in a Community Health System
Authors: Jones Bruce M , Plauche Emily , Smith Susan E , Bland Christopher M 
Published: January 2021

Abstract

Background
Penicillin allergy reconciliation is an important aspect of antimicrobial stewardship with ~10% of the population reporting a penicillin allergy. Our facility utilizes a Penicillin Allergy Reconciliation Program (PARP) led by an Infectious Diseases (ID) Pharmacist and pharmacy students to identify patients with penicillin allergies to reconcile and intervene when necessary. Information is collected by interview, electronic medical record (EMR) review, prescription outpatient fill history. This study evaluated reconciliations with and without a PARP in patients in a community health system.

Methods
This was a retrospective study that compared reconciliations performed on adult patients admitted at least once in 2019 with a self-reported penicillin allergy and ID physician consult at a hospital with a PARP (Institution 1) and one without a formal evaluation and intervention program (Institution 2) within the same community health system with same ID physicians. The primary outcome was documented reconciliation of a patient’s penicillin allergy during an inpatient visit in 2019. Reconciliation was defined as an edit or clarification (updating the severity, reaction, or comments section, as well as deleting) to a patient’s penicillin allergy in the EMR. The secondary outcome evaluated the percentage of total and ID consult patients with a penicillin allergy.

Results
There were 245 patients who met criteria and were included in the study, 113 from Institution 1 and 132 from Institution 2. For the primary outcome, there were 82 (72.6%) reconciliations at Institution 1 and 15 (11.4%) reconciliations at Institution 2 (p &lt; 0.001). Interventions at Institution 1 and 2 resulted in 74 EMR updates and 8 removals and 14 EMR updates and 1 removal, respectively. Reconciliation was performed on the same visit as the ID consult in 59/82 patients (72%) at Institution 1 and 11/15 patients (73.3%) at Institution 2. All reconciliations at Institution 2 were made by pharmacist (10) or nurses (5). For the secondary outcome, 10.9% of patients with an ID consult and 12.6% of all patients admitted in 2019 had a penicillin allergy (p=0.027).

Conclusion
A PARP led by an ID pharmacist and students was an effective method to perform penicillin allergy reconciliations, even in the presence of active ID consultation.

Disclosures
Bruce M. Jones, PharmD, BCPS, ALK-Abello (Research Grant or Support)Allergan/Abbvie (Speaker’s Bureau) Christopher M. Bland, PharMD, FCCP, FIDSA, BCPS, ALK Abello, Inc. (Grant/Research Support)Biomerieux (Consultant)Merck (Consultant, Grant/Research Support, Advisor or Review Panel member, Speaker’s Bureau)Tetraphase (Speaker’s Bureau)
833. Characteristics and Utilization Patterns of Colistin Compared with Newer Agents in Gram-Negative Infections
Authors: Marcella Stephen , Doremus Casey , Echols Roger 
Published: January 2021

Abstract

Background
Colistin has resurfaced in light of Gram-negative (GN) resistance. New antibiotics to treat antibiotic resistant GN infections (eg, ceftazidime-avibactam, ceftolozane-tazobactam, meropenem-vaborbactam [new agents]), have recently been approved but their use vs colistin is unclear. We compared the overall use of colistin and new agents from 2014 to 2018 in patient days on therapy (PDOT).

Methods
Data on non-cystic fibrosis patients from the Premier Healthcare Database was used. PDOT was tabulated quarterly for Premier hospitals and projected to the US population. A subset of data from 2016 to 2018 with microbiologically confirmed GN (MCGN) infections was selected for adult inpatients receiving ≥3 days of therapy with colistin, new agents, carbapenems, or extended-spectrum cephalosporins. The index infection was defined either as the first carbapenem-resistant (CR) or -sensitive infection if no CR infection occurred. Patients could be treated with ≥1 antibiotic per infection. Utilization was examined by pathogen and patient characteristics.

Results
PDOT with colistin decreased from 2015 to 2018, while new agents have increased (Figure). During 2015–2018, colistin and any of 3 new agents were used by 3,320 and 5,781 inpatients, respectively, of whom, 649 (20%) and 1,284 (22%) had MCGN pathogens. Colistin-treated patients were sicker than patients treated with new agents (Table), underlying renal disease was present in 34.5% vs 36.3 %, and median length of stay of 17 vs 15 days, respectively. Mean total hospital cost was $93,815 vs $84,013 for colistin and new agents, respectively. Mortality was greater in colistin patients (18% vs 12%; p&lt; 0.0001). CR infections constituted similar proportions of colistin and new agent use (79% vs 75%). Colistin accounted for 15.2% of CR Acinetobacter treatments and 9.7% of CR Enterobacterales (CRE) treatments compared with 4.5% and 12.8%, respectively, for new agents.
Figure. Projected Inpatient PDOT

Table.

Conclusion
Colistin use has decreased simultaneously with the introduction and increased use of new agents in the USA. Colistin was used more frequently in sicker patients and for Acinetobacter spp. infections than for CRE infections. Patients on colistin have worse outcomes, probably due to baseline differences in their health status.

Disclosures
Stephen Marcella, MD, Shionogi Inc. (Employee) Casey Doremus, MS, Shionogi Inc. (Employee) Roger Echols, MD, Shionogi Inc. (Consultant)
839. Epidemiology of Extended-Spectrum Beta-lactamase (ESBL) Producing Enterobacteriaceae in the South East Tennessee, October-December 2017
Authors: Muleta Daniel , Adre Cullen , Warner Benji-Byrd 
Published: January 2021

Abstract

Background
The increasing spread of drug resistant gram-negative organisms is one of the major public health challenges. ESBL-producing Enterobacteriaceae has become the most common multi drug resistant pathogen in the last three decades. These organisms confer resistance to most beta-lactam antibiotics, including penicillins, third generation cephalosporins, monobactams and tazobactam.

Methods
The Tennessee Health Department (TDH) collaborated with CDC to pilot population based surveillance of ESBL producing organisms in Maury, Wayne, Lewis and Marshall Counties during October to December 2017. A case was defined as isolation of Escherichia coli, Klebsiella pneumoniae, or Klebsiella oxytoca resistant to at least one extended-spectrum cephalosporin (ceftazidime, cefotaxime or ceftriaxone) and non-resistant to all carbapenem antibiotics from urine or normally sterile body sites from a resident of the surveillance catchment area. A line list of ESBL-producing organisms was received from the labs that serve the catchment population. Case report forms were completed for the first ESBL culture collected from a single patient in a 30 day-period.

Results
A total of 154 cases were identified during the study period. E.coli constitutes 92.2% of the ESBL producing organisms followed by Klebsiella pneumonia (5.2%) and K. oxytoca (2.6%). The estimated annual incidence rate was 400.7 per 100,000 population which is more than twice of the average rates of other sites that conducted similar studies. The most common isolate source was urine (97%), and 81.2% of all cases were female. Patient ages ranged from 3-99 years, with average of 67 years. Thirty-two isolates underwent additional sequence typing and 76.7% (23) of the isolates were ST 131. 21 (91.3%) of ST-131 isolates were resistant to ciprofloxacin.

Conclusion
The study revealed that the incidence of ESBL producing organisms is very high in the Tennessee study area compared to other sites. The most common ESBL-producing pathogen was found to be ST 131 and most of these were resistant to ciprofloxacin suggesting that resistance to fluoroquinolone may be co-transmitted in ESBL producing pathogens through plasmids. Continued surveillance of molecular epidemiology is important to guide the prevention of the spread of drug resistant pathogens.

Disclosures
All Authors: No reported disclosures
840. First Report of Pseudomonas aeruginosa Isolates Harboring the CTX-M2 and PER genes in Algeria
Authors: Almpani Marianna , Tchakal-Mesbahi Asma , Metref Merzak , Singh Vijay K , Rahme Laurence G 
Published: January 2021

Abstract

Background
Despite significant improvements in burn care, multidrug-resistant (MDR) Pseudomonas aeruginosa (PA) remains one of the most common causes of life-threatening infections in patients suffering from thermal injuries. The objective of this study is to investigate the prevalence of MDR PA producing Extended-Spectrum Beta-lactamases (ESBLs) and metallo-beta-lactamases (MBLs) in burn patients in Algeria.

Methods
Between April 2016 and October 2019, 47 non-redundant isolates of PA were collected from 47 burn patients admitted to the Department of Burns at the Military Hospital of Algiers in Algeria. Antibiotic susceptibility testing was performed by agar diffusion and the Phoenix automated method. Resistance genes were identified by PCR, and molecular typing of isolates was carried out by enterobacterial repetitive intergenic consensus (ERIC) sequences-polymerase chain reaction (PCR).

Results
Among the 47 non-redundant MDR PA strains isolated, 59.57% were phenotypically ESBLs-positive, and 100% were phenotypically MBL-positive. The ESBL-positive isolates were subsequently screened for five groups of bla genes encoding ESBL-type enzymes, namely CTX-M2, PER, TEM, SHV, VEB, and GES. Out of the 28 ESBL-producing strains, 23 (82.14%) were CTX-M2 positive; 18 (38.29%) were PER positive, and 16 (34.04%) were TEM positive, while 5 (17.9%) were co-harboring CTX-M2, TEM, and PER genes. The SHV, VEB, and GES genes were not detected in any of the ESBL positive isolates. Since all isolates were MBL-positive, all 47 strains were screened for the NDM-1, IMP, VIM genes that produce MBLs; however, none of these genes were detected. Additional screening for the OprD gene demonstrated that 45 (95.74%) of the isolates were positive for this gene. Finally, ERIC PCR revealed 6 distinct PA clones among the CTX-M2 positive strains.
Table 1: Occurrence of beta-lactamase genes in relation to the antimicrobial susceptibility profiles of the PA isolates.

Conclusion
This is the first report of CTX-M2-producing PA in the North Africa region and the first to detect CTX-M2-positive and PER-positive PA clinical isolates in Algeria, therefore demonstrating the spread of such MDR strains in this part of the world. Identification of genotypic alterations that confer antibiotic resistance is critical in determining effective antimicrobial strategies. Hence, these findings could potentially guide antibiotic choice decisions.
World map with countries where PER- and CTX-M2-postive Pseudomonas aeruginosa isolates have been reported.

Disclosures
All Authors: No reported disclosures
844. Nosocomial Pseudomonas aeruginosa Blood-Stream Infections; Susceptibility Pattern and Mortality at a Tertiary Care Centre in Edmonton, Alberta, Canada
Authors: Savaryn Bohdan , Van Der Walt Peet , Smith Stephanie 
Published: January 2021

Abstract

Background
Pseudomonas aeruginosa is one of the leading gram negative nosocomial pathogens, causing severe infections including blood-stream infections (BSI) with high mortality rates. (1). Multi-drug resistant P. aeruginosa (MDRPA) infection rates are reported to be increasing (2) and have been associated with increased mortality (3). This study aims to review the susceptibility pattern and trend of P. aeruginosa BSIs and mortality and identify patients at increased risk of BSI with a resistant P. aeruginosa isolate. This data has important treatment implications.

Methods
Cases of nosocomial P. aeruginosa bacteremia were prospectively identified at the University of Alberta, Edmonton, Alberta, Canada by the infection prevention and control surveillance program between January 1, 2007 and December 31, 2018. Patient charts were retrospectively reviewed to collect microbiological, clinical, and epidemiological information.

Results
148 cases of P. aeruginosa BSI were identified over a 12-year period between January 2007 and December 2018. There were 19 cases of MDRPA BSI and 9 cases of XDRPA BSI. The incidence of P. aeruginosa BSI was 0.47 per 10,000 patient days and remained relatively stable over the study period. 66.9% of cases occurred in men. The mean age was 60 years. The average length of stay prior to bacteremia was 42 days. The overall 30-day mortality following P. aeruginosa BSI was 36.4%. Risk factors for increased 30-day mortality included: pulmonary source of infection (OR 4.26, p &lt; 0.001), bacteremia with extremely drug resistant Pseudomonas aeruginosa (XDRPA) (p &lt; 0.0001), and diabetes (OR 2.24, p &lt; 0.05). BSI with MDRPA was not an independent risk factor for increased mortality. Significant risk factors for bacteremia with an MDRPA or XDRPA were length of stay &gt; 28 days (OR 4.22, p &lt; 0.001) and hemodialysis (OR 8.92, p &lt; 0.000001).
Annual hospital acquired P. aeruginosa blood-stream infections from 2007-2018

Antibiogram of P. aeruginosa blood-stream isolates from 2007-2018

Conclusion
The incidence of P. aeruginosa BSI as well as the rate of MDRPA and XDRPA BSI have remained stable at our centre between 2007 and 2018. We found that BSI with XDRPA but not MDRPA alone was a significant risk factor for mortality. Risk factors for BSI with a resistant P. aeruginosa strain may be considered to guide empiric therapy.

Disclosures
All Authors: No reported disclosures