bluuebunny/crossref_metadata_2025_split huggingface dataset:
671. Same Day Identification of Enterobacteriaceae Directly from Urine Samples
Authors: Kon Shelley E , Giddins Sara , Yushkevich Irina , Fuchs Martin , Irwin Amy , Metzger Steve , Price Connie S 
Published: January 2021

Abstract

Background
Urinary tract infections (UTIs) are one of the most common infections, associated with 10.5 million outpatient visits annually. Fast and accurate identification (ID) of bacteria causing a UTI would allow for immediate targeted therapy, as opposed to conventional methods which take one to three days. The Accelerate Pheno® system (ACC, Accelerate Diagnostics Inc., Tucson, AZ, USA) provides microbial ID and susceptibility (AST) from positive blood cultures. Our objective was to determine ACC’s potential to quickly ID bacterial pathogens directly from urine.

Methods
Remnant urine samples with &gt;100K colony forming units (CFU)/mL of gram-negative bacteria as determined by quantitative plating were obtained from the clinical lab. 1.5ml of urine was dispensed into a capsule and loaded onto the Accelerate PhenoPrep™ module. This module automatically performs wash steps to separate bacteria from human cells and other debris. The processed sample was loaded onto ACC for analysis using a custom designed assay which detects the presence of bacteria and employs an Enterobacteriaceae family specific FISH probe. The results were compared to standard of care ID results.

Results
There were 10 E. coli and 1 C. koseri among the eleven samples tested. Baseline concentration of samples immediately prior to testing ranged from 2.5 x 106 to 1.08 x 1010 CFU/mL (average 4.19 x 109). After specimen processing, average concentration was 2.14 x 109 CFU/mL and average recovery was 42.83%. ACC detected bacteria and identified it as Enterobacteriaceae in 11/11 samples (100%). Average sample prep time was 55 min. Average time to Enterobacteriaceae ID was 8.6 hrs. Average total time to ID, including specimen processing, was 9.5 hrs.
Table 1: Results of Direct from Urine Testing

Conclusion
ACC identified Enterobacteriaceae directly from remnant urine specimens in an average of 9.5 hours, approximately 24 to 48 hours faster than conventional methods. ACC was able to be adapted for use in urine samples. Future directions include improving the assay to identify bacteria to the species level and adding AST testing. This shows promise in providing fast actionable UTI diagnosis, allowing for tailored antibiotic therapy.
*This information concerns a use that has not been approved or cleared by the Food and Drug Administration.

Disclosures
Martin Fuchs, BSEE, MSEE, Accelerate Diagnostics (Employee) Steve Metzger, BA, Accelerate Diagnostics (Employee)
673. Updated CLSI Ciprofloxacin Breakpoints from a Multicenter Assessment for Enterobacterales, Salmonella spp. and Pseudomonas aeruginosa Using MicroScan Dried Gram Negative MIC Panels
Authors: Traczewski Maria M , Beasley Denise , Harrington Amanda , DesJarlais Sharon , Garner Omai , Hastey Christine , Brookman Regina , Lockett Zabrina , Chau Jennifer 
Published: January 2021

Abstract

Background
Updated US FDA/CLSI ciprofloxacin breakpoints were evaluated against data from a multicenter clinical study with Enterobacterales, Salmonella spp. and P. aeruginosa on a MicroScan Dried Gram-negative MIC (MSDGN) Panel. MIC results were compared to results obtained with frozen broth microdilution panels prepared according to CLSI methodology.

Methods
MSDGN panels were evaluated at three clinical sites by comparing MIC values obtained using the MSDGN panels to MICs utilizing a CLSI broth microdilution reference panel. Data from the combined phases of efficacy and challenge included 803 Enterobacterales, Salmonella spp. and P. aeruginosa clinical isolates tested using the turbidity and Prompt® methods of inoculation. To demonstrate reproducibility, a subset of 12 organisms were tested on MSDGN panels at each site during reproducibility. MSDGN panels were incubated at 35 ± 1ºC and read on the WalkAway System, the autoSCAN-4 instrument, and visually. Read times for the MSDGN panels were at 16-20 hours. Frozen reference panels were prepared and read according to CLSI methodology. FDA and CLSI breakpoints (µg/mL) used for interpretation of MIC results were: Enterobacterales ≤ 0.25 S, 0.5 I, ≥ 1 R; Salmonella spp. ≤ 0.06 S, 0.12-0.5 I, ≥ 1 R; P. aeruginosa ≤ 0.5 S, 1 I, ≥ 2 R.

Results
Essential and categorical agreement was calculated compared to frozen reference panel results. Results for isolates tested during efficacy and challenge with Prompt inoculation and manual read are as follows:

Conclusion
Ciprofloxacin MIC results for Enterobacterales, Salmonella spp., and P. aeruginosa obtained with the MSDGN panel correlate well with MICs obtained using frozen reference panels using updated FDA/CLSI interpretive criteria in this multicenter study.
* PROMPT® is a registered trademark of 3M Company, St. Paul, MN USA.
BEC, the stylized logo and the BEC product and service marks mentioned herein are trademarks or registered trademarks of Beckman Coulter, Inc. in the US and other countries.

Disclosures
Maria M. Traczewski, BS MT (ASCP), Beckman Coulter (Scientific Research Study Investigator) Denise Beasley, BS, Beckman Coulter (Other Financial or Material Support, Research personnel) Amanda Harrington, PhD, Beckman Coulter (Scientific Research Study Investigator) Sharon DesJarlais, BS, Beckman Coulter (Other Financial or Material Support, Research personnel) Omai Garner, PhD, D(ABMM), Beckman Coulter (Scientific Research Study Investigator) Christine Hastey, PhD, Beckman Coulter (Employee) Regina Brookman, BS, Beckman Coulter (Employee) Zabrina Lockett, MS, Beckman Coulter (Employee) Jennifer Chau, PhD, Beckman Coulter (Employee)
675. Evaluation of PLST for Clostridioides difficile Sequence-based Strain Typing
Authors: Edlind Tom , Redding Laurel 
Published: January 2021

Abstract

Background
Clostridioides difficile is a leading cause of healthcare-associated infection (HAI), most often following antibiotic therapy. The source of these infections may be endogenous or nosocomial; effective intervention requires distinquishing between these, which in turn requires strain typing. Numerous methods have been developed for C. difficile typing, ranging from length-based ribotyping and MLVA to whole genome sequencing. However, none are routinely used in clinical settings due to low resolution, high cost, technical complexity, or requirement for cultured isolates. The application of polymorphic locus sequence typing (PLST) to epidemiological analysis of HAI and foodborne infections has recently been described; here this approach is extended to C. difficile.

Methods
Tandem repeats were bioinformatically identified in the genome sequence of ribotype 027 strain R20291. These were screened by BLASTN of GenBank databases for the most polymorphic locus, which identified CdMT1 (Mbp 3.149). DNA was purified from colonies or environmental (Banana Broth) cultures; bead-beating and PCR inhibitor removal steps were required for consistent results.

Results
CdMT1 encompassed MLVA repeat C6cd which, based on length alone, yielded the highest diversity index (DI) of 0.96. In contrast, CdMT1 sequence analysis yielded DI of &gt;0.99. Comparison to ribotype further illustrated high level resolution; e.g., 9 ribotype 027 strains were resolved into 8 CdMT1 alleles. For initial laboratory evalulation, veterinary C. difficile isolates (44 canine, 4 bovine) were CdMT1 typed. Bioinformatic analysis of the 48 sequences resolved 24 CdMT1 alleles, including 8 clusters of 2 to 6 canine strains. Six of these clusters represented isolates from individual puppies in the same litter, or from different litters but the same household, while the bovine isolates formed a phylogenetically distinct group. Using the same DNA purification protocol, CdMT1 typing demonstrated compatibility with C. difficile-spiked stool samples and Banana Broth environmental cultures.

Conclusion
CdMT1 typing represents a potentially useful tool for outbreak detection and investigation in healthcare facilities, particularly in light of its compatibility with both stool and environmental samples.

Disclosures
Tom Edlind, PhD, MicrobiType LLC (Employee, Scientific Research Study Investigator)
680. The Use of Plasma Next-Generation Sequencing Test in the Management of Immunocompetent and Immunocompromised Patients – A Single Center Retrospective Study
Authors: Francisco Denise Marie A , Woc-colburn Laila , Carlson Travis J , Lasco Todd , Barrett Miriam B , Mohajer Mayar Al 
Published: January 2021

Abstract

Background
Microbiological culture data is a longstanding gold standard in diagnostics. Unfortunately, yield from cultures have been inconsistent and slow, prompting the need for newer tests including the plasma-based next-generation sequencing (NGS) tool. This study aims to describe the use of NGS and the corresponding change in management.

Methods
A descriptive retrospective study was done on hospitalized adults at CHI-Baylor St. Luke’s in Houston, Texas with NGS tests from Jan 1, 2017 to Dec 31, 2018.
Graph 1 - Next Generation Sequencing Test Breakdown

Results
There were 167 NGS tests performed. Most patients were non-Hispanic (n=129) Caucasian (n=106) males (n=116) with a mean age of 52. Furthermore, 61 were immunocompromised patients [solid organ transplant (n=30), HIV-AIDS (n=14) and rheumatology patients on immunosuppression (n=12)].
During the study, the hospital staff prepared a list of indications for NGS testing including: systemic or deep seated infection where a biopsy or other workup is negative or not possible (n=50), fever of unknown origin (n=26), culture negative endocarditis (n=15), HIV/AIDS with fever (n=10), transplant patient with fever (n=5). There were 60 cases where the indications were not on this list (36%).
Results showed that 118/167 (71%) were positive. The most common organisms identified were gram-negative bacteria (54/118; 46%) followed by viruses (49/118; 42%), gram-positive bacteria (48/118; 41%), fungi (16/118; 14%), atypical bacteria (9/118; 8%), mycobacterium (4/118; 3%), and parasites (4/118; 3%). Blood cultures were concurrently obtained in 148/167 (89%) of the cases and returned negative in 137/148 (93%) of cases.
In terms of change of management, the largest change was found in glycopeptide use (36 fewer patients after NGS results). Next was on anti-mycobacterial drugs where 27 were added among 8 instances. Only 36 patients were taken off antibiotics, even though 49 patients had negative results. In total, 120 out of 160 cases had antibiotic changes.
Table 1 - Demographic and Laboratory Characteristics

Graph 2 - Change in Number of Antibiotics (Total: Before and After)

Graph 3 - Indications for Testing and Change in Number of Antibiotics

Conclusion
We observed a large decrease in glycopeptide use after NGS results which suggests physicians’ comfort in withdrawing MRSA coverage. In addition, anti-mycobacterial coverage increased corresponding to early mycobacterial detection with NGS. This study highlights the importance of clinical judgement in the age of rapid diagnostics.

Disclosures
All Authors: No reported disclosures
681. Induction Immunosuppression Selection in People Living with HIV Undergoing Deceased Donor Kidney Transplantation: U.S. National Trends from 2000 to 2018
Authors: Cano Edison J , Mullan Aidan , Vijayvargiya Prakhar , Shweta F N U , Gurram Pooja , Rizza Stacey , Mahmood Maryam , Badley Andrew , Dean Patrick , Cummins Nathan 
Published: January 2021

Abstract

Background
Human Immunodeficiency Virus (HIV) outcomes have significantly improved at the expense of other age-related diseases including chronic kidney disease. Early reports of people living with HIV (PLWH) undergoing deceased-donor kidney transplantation (DDKT) showed poor outcomes, but these have notably improved after introduction of antiretrovirals. Despite years of experience, the optimal induction immunosuppression (IIS) in PLWH remains subject of debate. Large-scale studies describing the current ISS practices in PLWH undergoing DDKT are lacking. Here, we describe the U.S. national trends of IIS used in PLWH undergoing DDKT from 2000 to 2018 using the United Network of Organ Sharing (UNOS) database.

Methods
We analyzed the UNOS database to determine the selection of IIS in PLWH undergoing first-time DDKT between 1/1/2000 and 12/31/2018. Cases with unknown HIV status at the time of transplant were excluded. Age, sex and demographics were analyzed. The regimen used for IIS was compared based on HIV serostatus and the change in induction regimen was trended over time.

Results
A total of 139,650 cases underwent DDKT during the study period. Among these, 1,384 were identified as HIV-positive. PLWH were significantly younger than HIV-negative (49±10 years vs. 51.6 ± 15.3 years; p&lt; 0.001) (Table 1). A greater proportion of men was seen in the PLWH group compared to HIV-negative persons (76.2% vs. 60.4%; p&lt; 0.0001). In the HIV-negative group, 12.1% undergoing DDKT did not receive IIS compared to 16.4% in PLWH (p&lt; 0.0001). Medications that have significantly increased in use with years in PLWH included rabbit anti-thymocyte globulin (rATG), steroids, and basiliximab (3.54, 3.25, 2.28, respectively; p&lt; 0.001). On our trend analysis (Figure 1), the percentage of PLWH receiving any IIS is increasing by 4.04% each year (p&lt; 0.001).
Table 1

Figure 1

Conclusion
Our study suggests that IIS is an increasing practice in PLWH undergoing DDKT, predominantly using rATG, steroids, and basiliximab. Understanding the current practices might lead to further studies to determine the long-term outcomes after different induction regimens in PLWH.

Disclosures
All Authors: No reported disclosures
687. Iatrogenic Kaposi’s Sarcoma Following Treatment with Vedolizumab
Authors: Ajao Susanne O , Shaaban Hamid , Jayasingam Rajasingam 
Published: January 2021

Abstract

Background
Kaposi’s sarcoma (KS) is a vascular tumor caused by human herpes virus-8 infection (HHV-8) commonly involving the skin. We report a case of a patient with controlled HIV who developed Kaposi’s sarcoma on vedolizumab.
Darkened hyperkeratotic plaque on his left medial foot

Methods
A 39-year-old homosexual male with a history of Ulcerative Colitis (UC), Hodgkin’s lymphoma in remission and HIV presented with complaints of abdominal pain and bloody diarrhea. He had new tender lesions on his left foot which was absent at his previous admission a month ago. The lesions started as macules and later progressed to tender lesions. Mesalamine and oral corticosteroids were previously prescribed without symptomatic relief and he was started on vedolizumab 2 months ago. On physical exam he had abdominal tenderness, tender cervical and inguinal lymph nodes, and dark macules on his feet. Digital rectal exam revealed bloody mucoid stool. Laboratory showed white blood cell count of 12,600/mm3, ESR of 132 mm/hr and CRP of 4.6 mg/dL. His CD4 T-cell count was 873 cells/mm3 and viral load was 50 copies per milliliter. Cervical lymph node biopsy showed polymorphous population of lymphocytes but was negative for malignant cells. Biopsy of the foot plaques showed atypical intradermal vascular and spindle cell proliferation positive for HHV-8 and for vascular marker CD34. The results were consistent with the diagnosis of KS. Serology was also positive for HHV-8 with high viral titers of 74 copies/mL. Colonoscopy showed severe proctitis with deep ulcerations in a continuous pattern in the rectum with a normal sigmoid colon. Follow up colonoscopy showed improved proctitis and he was started on doxorubicin to treat KS with improvement of the foot lesion a month later following treatment.
Dark macules on the sole of both feet

Figure 3a: Spindle cells with irregular small vessel proliferation and red blood cell extravasation between tumor cells Figure 3b: Immunohistochemical stain showing HHV-8 expression of spindle cells

Improvement of the foot lesion

Results
Vedolizumab is a monoclonal antibody that prevents the recruitment of lymphocytes to the inflamed tissue. It is approved for the treatment of IBD and has shown efficacy and safety. The iatrogenic form of Kaposi’s sarcoma occurs in patients on immunosuppressive therapy, as this patient.

Conclusion
Patients with IBD on immunosuppressive drugs should be followed up closely and screened for latent viral infections prior to initiating therapy. As in the patient, HHV-8 should be recognized as a likely underlying opportunistic infection in immunocompromised patients with IBD.

Disclosures
All Authors: No reported disclosures
689. Nasal versus Nasopharyngeal Sample Collection for Diagnostic Nucleic Acid Amplification Testing for Influenza A, Influenza B, and Respiratory Syncytial Viruses
Authors: Schaack Grace A , Jung-Hynes Brittney , Chen Derrick 
Published: January 2021

Abstract

Background
Nucleic acid amplification testing (NAAT) for influenza A virus (IAV), influenza B virus (IBV), and respiratory syncytial virus (RSV) is a standard component of diagnosis of infections with these pathogens. At our institution, current standard of practice is to collect nasopharyngeal (NP) samples for such NAAT. In an effort to provide clinicians and patients a simpler, more comfortable sample collection option, we evaluated the use of nasal samples for NAAT, compared to NP samples.

Methods
Both nasal and NP specimens were collected from each of 58 patients seen in our emergency department (January – March 2020). NP samples were collected using minitip FLOQswabs; nasal samples were collected using regular or minitip FLOQswabs. Nasal and NP samples were processed using the same protocol and tested for influenza viruses and RSV using the Cepheid GeneXpert (Xpress Flu/RSV) platform.

Results
In total, 20 NP samples tested negative for virus and 38 tested positive (16 IAV-positive, 14 IBV-positive, 8 RSV-positive). There were 3 cases (5% of total cases) in which qualitative (positive/negative) results from the corresponding nasal samples were not in agreement with results derived from NP samples. These were considered false-negative results; one such discrepancy was resolved upon re-testing the same samples. Overall positive percent agreement between nasal- and NP-derived results was 92% (35/38), and negative percent agreement was 100% (20/20). Among samples testing positive for virus by both NP and nasal sampling methods, we found that the average cycle threshold (Ct) value for IAV detection was 5.1 cycles (n = 16, SEM = 0.83) higher for nasal samples than for NP samples. The average Ct for IBV detection was 3.3 cycles (n = 12, SEM = 1.87) higher for nasal than for NP samples. The average Ct for RSV detection was 1.9 cycles (n = 7, SEM = 1.57) higher for nasal than for NP samples.

Conclusion
These results suggest that recovery of viral RNA from nasal samples is lower than that from nasopharyngeal samples, particularly for influenza viruses. This decreased detection of viral RNA from nasal samples may explain the false-negative results seen in our discrepant cases. These data suggest that a decrease in recovery of viral RNA by nasal sampling may translate to decreased diagnostic accuracy.

Disclosures
All Authors: No reported disclosures
692. Secondary Infections and Coinfections in Coronavirus Disease 2019 (COVID-19)
Authors: Kaur Ikwinder P , Mughal Mohsin S , Dalmacion Denise L , Jaffery Ali , Koyoda Sai , Kramer Violet , Granet Kenneth , Eng Margaret 
Published: January 2021

Abstract

Background
While a common phenomenon in other viral illnesses, data regarding coinfection/superinfections in Coronavirus Disease 2019 (COVID-19) is limited and emerging. Superinfections may contribute to the overall high mortality in those suffering from severe COVID19. We aimed to study the rate of coinfections and secondary bacterial/fungal infections among SARS-CoV-2 positive cases in a community hospital.

Methods
This is a single-centre IRB approved, retrospective observational study. Adult patients with laboratory-confirmed SARS-CoV-2 by Real-Time Reverse Transcriptase–Polymerase Chain Reaction assay of nasopharyngeal swabs admitted from March 1st to April 20th 2020 were included. Relevant clinical and laboratory data were manually collected from electronic medical records.

Results
A total of 129 patients were included in the study. 91 patients had a respiratory pathogen panel PCR on admission. This panel includes testing for influenza, parainfluenza virus, respiratory syncytial virus, coronavirus, adenovirus, rhinovirus, Bordetella pertussis, Bordetella parapertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae. Only one patient was positive for coinfection with the parainfluenza virus. None of them was found to be positive for bacterial coinfection at admission. Thirteen patients (10.1%) had secondary bacterial or fungal infections that developed during their respective hospital stays, 12 of them were critically ill. The mean duration from admission to the onset of secondary infection was 13 days.
Positive Blood Cultures

Positive Lower Respiratory Tract Cultures

Conclusion
Our data revealed that the rate of viral coinfection was 1.1 % and bacterial coinfection was 0% at admission. Study timing can play a role as upper respiratory virus infection rate is low in the population during March and April. Secondary infections were found to be common in patients admitted to the ICU. Potential explanations for this include compromised immunity in severely ill patients, extended ICU stay, central venous catheters and endotracheal intubation. It is evident that with severe COVID-19 illness, an extended hospital course often ensues, leading to increased risk of secondary infections and contributing to the overall high mortality of these patients.

Disclosures
All Authors: No reported disclosures